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Gold in PDB 3hp3: Crystal Structure of CXCL12

Protein crystallography data

The structure of Crystal Structure of CXCL12, PDB code: 3hp3 was solved by J.W.Murphy, E.Lolis, Y.Xiong, H.Yuan, G.Crichlow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.18 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.834, 117.468, 134.501, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 28

Gold Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Gold atom in the Crystal Structure of CXCL12 (pdb code 3hp3). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 12 binding sites of Gold where determined in the Crystal Structure of CXCL12, PDB code: 3hp3:
Jump to Gold binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Gold binding site 1 out of 12 in 3hp3

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Gold binding site 1 out of 12 in the Crystal Structure of CXCL12


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 1 of Crystal Structure of CXCL12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au107

b:1.0
occ:0.48
NE2 A:GLN48 2.8 31.5 1.0
ND1 A:HIS25 2.9 32.4 1.0
CB A:HIS25 3.7 23.0 1.0
CG A:HIS25 3.7 40.0 1.0
CB A:ARG41 3.8 30.2 1.0
N A:ARG41 3.9 28.9 1.0
CE1 A:HIS25 3.9 35.2 1.0
CD A:GLN48 4.0 37.3 1.0
O A:HIS25 4.0 25.8 1.0
NE A:ARG41 4.1 59.5 1.0
O A:VAL39 4.2 17.0 1.0
C A:HIS25 4.2 18.7 1.0
CB A:LYS27 4.3 22.3 1.0
CG B:PRO32 4.4 24.6 1.0
C A:ALA40 4.4 18.1 1.0
CA A:ARG41 4.5 15.4 1.0
OE1 A:GLN48 4.5 33.9 1.0
CA A:HIS25 4.6 19.2 1.0
N A:LEU26 4.6 26.8 1.0
CA A:ALA40 4.7 26.7 1.0
C A:VAL39 4.7 22.3 1.0
CB B:PRO32 4.8 25.3 1.0
CG1 A:VAL39 4.8 23.2 1.0
N A:LYS27 4.8 25.4 1.0
CD A:ARG41 4.8 47.4 1.0
NH1 A:ARG41 4.8 69.6 1.0
C A:LEU26 4.8 28.4 1.0
CD2 A:HIS25 4.9 36.0 1.0
CZ A:ARG41 4.9 65.9 1.0
CA A:LEU26 4.9 27.4 1.0
CD A:LYS27 4.9 47.0 1.0
CG A:ARG41 4.9 30.9 1.0
NE2 A:HIS25 5.0 46.4 1.0
N A:ALA40 5.0 25.1 1.0

Gold binding site 2 out of 12 in 3hp3

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Gold binding site 2 out of 12 in the Crystal Structure of CXCL12


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 2 of Crystal Structure of CXCL12 within 5.0Å range:

Gold binding site 3 out of 12 in 3hp3

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Gold binding site 3 out of 12 in the Crystal Structure of CXCL12


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 3 of Crystal Structure of CXCL12 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Au106

b:81.1
occ:0.40
ND1 B:HIS25 2.6 43.9 1.0
CE1 B:HIS25 3.3 45.3 1.0
NE2 B:GLN48 3.3 39.2 1.0
O B:HOH205 3.4 42.0 1.0
CG B:HIS25 3.7 40.7 1.0
O B:VAL39 3.8 16.4 1.0
O B:HIS25 3.8 23.0 1.0
N B:ARG41 3.9 16.9 1.0
CB B:LYS27 4.0 21.2 1.0
C B:HIS25 4.1 26.3 1.0
CB B:HIS25 4.1 22.8 1.0
CB B:ARG41 4.2 22.7 1.0
CG1 B:VAL39 4.2 40.1 1.0
C B:VAL39 4.3 15.9 1.0
C B:ALA40 4.3 13.4 1.0
N B:LYS27 4.3 17.6 1.0
C B:LEU26 4.4 25.2 1.0
CA B:ALA40 4.4 14.2 1.0
N B:LEU26 4.4 14.5 1.0
NE2 B:HIS25 4.5 51.7 1.0
CD B:GLN48 4.5 47.4 1.0
CG A:PRO32 4.5 31.3 1.0
CA B:LEU26 4.5 28.4 1.0
NE B:ARG41 4.5 63.4 1.0
N B:ALA40 4.6 14.3 1.0
CA B:ARG41 4.7 12.5 1.0
CD2 B:HIS25 4.7 47.9 1.0
CA B:HIS25 4.7 27.8 1.0
CE B:LYS27 4.8 47.3 1.0
CA B:LYS27 4.8 22.8 1.0
O B:LEU26 4.8 27.4 1.0
CB B:VAL39 4.8 22.7 1.0
CG B:GLN48 4.9 37.1 1.0

Gold binding site 4 out of 12 in 3hp3

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Gold binding site 4 out of 12 in the Crystal Structure of CXCL12


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 4 of Crystal Structure of CXCL12 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Au105

b:1.0
occ:0.87
CB C:HIS25 3.2 17.4 1.0
C C:HIS25 3.8 13.0 1.0
O C:HIS25 3.9 27.3 1.0
CB C:LYS27 3.9 23.6 1.0
CA C:HIS25 4.2 26.8 1.0
N C:LEU26 4.2 27.6 1.0
C C:LEU26 4.3 29.5 1.0
N C:LYS27 4.3 22.5 1.0
NE2 C:GLN48 4.4 31.2 1.0
O C:VAL39 4.5 17.5 1.0
N C:ARG41 4.5 15.8 1.0
ND2 A:ASN67 4.6 0.3 1.0
O C:LEU26 4.6 31.0 1.0
CB C:ARG41 4.6 23.5 1.0
CA C:LEU26 4.6 24.6 1.0
CA C:LYS27 4.7 26.2 1.0
N C:HIS25 5.0 29.2 1.0

Gold binding site 5 out of 12 in 3hp3

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Gold binding site 5 out of 12 in the Crystal Structure of CXCL12


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 5 of Crystal Structure of CXCL12 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Au101

b:98.1
occ:0.45
ND1 D:HIS25 2.6 38.3 1.0
NE2 D:GLN48 3.3 37.1 1.0
CG D:HIS25 3.5 27.6 1.0
O D:HIS25 3.6 22.3 1.0
CE1 D:HIS25 3.6 34.6 1.0
CB D:HIS25 3.6 15.9 1.0
C D:HIS25 3.7 19.3 1.0
N D:ARG41 3.7 19.4 1.0
CB D:ARG41 3.8 24.1 1.0
CB D:LYS27 3.8 26.9 1.0
NH2 D:ARG41 3.8 66.6 1.0
O D:VAL39 3.8 17.6 1.0
N D:LYS27 4.0 18.0 1.0
N D:LEU26 4.0 13.9 1.0
C D:LEU26 4.1 20.0 1.0
CA D:LEU26 4.2 14.4 1.0
CA D:HIS25 4.3 13.5 1.0
C D:ALA40 4.3 15.7 1.0
CA D:ARG41 4.4 13.3 1.0
CD D:GLN48 4.6 38.0 1.0
CA D:LYS27 4.6 24.1 1.0
CA D:ALA40 4.6 18.8 1.0
C D:VAL39 4.6 26.0 1.0
O D:LEU26 4.6 28.0 1.0
CD2 D:HIS25 4.7 25.2 1.0
NE2 D:HIS25 4.7 35.1 1.0
CZ D:ARG41 4.8 67.1 1.0
CD D:ARG41 4.8 44.8 1.0
CG D:ARG41 4.8 28.8 1.0
N D:ALA40 4.9 27.8 1.0

Gold binding site 6 out of 12 in 3hp3

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Gold binding site 6 out of 12 in the Crystal Structure of CXCL12


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 6 of Crystal Structure of CXCL12 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Au102

b:96.7
occ:0.52
ND1 E:HIS25 3.1 54.8 1.0
NE2 E:GLN48 3.5 30.0 1.0
CB E:HIS25 3.8 22.7 1.0
O E:HIS25 3.8 24.9 1.0
CG E:HIS25 3.9 50.7 1.0
CB E:LYS27 4.0 26.5 1.0
C E:HIS25 4.0 21.7 1.0
O E:VAL39 4.1 18.2 1.0
N E:ARG41 4.1 18.5 1.0
CB E:ARG41 4.1 19.8 1.0
CE1 E:HIS25 4.2 49.7 1.0
N E:LYS27 4.3 10.0 1.0
N E:LEU26 4.3 17.6 1.0
C E:LEU26 4.4 27.4 1.0
O E:HOH151 4.5 43.9 1.0
CA E:HIS25 4.6 23.8 1.0
CA E:LEU26 4.6 20.6 1.0
CA E:ARG41 4.7 17.9 1.0
O E:LEU26 4.8 24.3 1.0
CA E:LYS27 4.8 18.7 1.0
CD E:GLN48 4.8 39.1 1.0
C E:ALA40 4.8 18.6 1.0
O G:HOH105 4.9 26.5 1.0
C E:VAL39 4.9 19.1 1.0
CA E:ALA40 5.0 15.7 1.0

Gold binding site 7 out of 12 in 3hp3

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Gold binding site 7 out of 12 in the Crystal Structure of CXCL12


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 7 of Crystal Structure of CXCL12 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Au108

b:0.2
occ:0.73
CD2 E:HIS17 3.2 54.3 1.0
O E:SER16 3.7 47.1 1.0
CG E:HIS17 3.7 52.5 1.0
CA E:HIS17 3.9 37.8 1.0
NE2 E:HIS17 3.9 57.5 1.0
CB E:HIS17 4.1 46.9 1.0
C E:SER16 4.5 41.1 1.0
ND1 E:HIS17 4.5 57.4 1.0
CE1 E:HIS17 4.6 59.4 1.0
C E:HIS17 4.7 32.7 1.0
N E:HIS17 4.7 33.0 1.0

Gold binding site 8 out of 12 in 3hp3

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Gold binding site 8 out of 12 in the Crystal Structure of CXCL12


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 8 of Crystal Structure of CXCL12 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Au103

b:0.7
occ:0.49
ND1 G:HIS25 2.8 74.9 1.0
CG G:HIS25 3.5 67.0 1.0
CB G:HIS25 3.5 29.0 1.0
CE1 G:HIS25 3.8 77.7 1.0
C G:HIS25 3.8 30.7 1.0
O G:HIS25 3.8 34.6 1.0
N G:LEU26 4.0 24.0 1.0
N G:ARG41 4.1 16.5 1.0
O G:VAL39 4.1 19.1 1.0
O G:HOH163 4.1 40.8 1.0
CG G:LYS27 4.2 21.1 1.0
CA G:ALA40 4.3 23.1 1.0
C G:ALA40 4.3 15.6 1.0
CA G:HIS25 4.3 19.3 1.0
N G:LYS27 4.4 14.2 1.0
CA G:LEU26 4.4 29.8 1.0
CB G:LYS27 4.5 20.9 1.0
C G:LEU26 4.5 18.7 1.0
CB G:ARG41 4.5 16.8 1.0
NE2 G:GLN48 4.6 37.4 1.0
O E:HOH70 4.6 45.7 1.0
CD2 G:HIS25 4.6 65.4 1.0
C G:VAL39 4.7 17.8 1.0
NE2 G:HIS25 4.7 82.1 1.0
N G:ALA40 4.7 13.6 1.0
CG E:PRO32 4.8 29.0 1.0
CB E:PRO32 4.9 27.1 1.0
CA G:ARG41 4.9 13.0 1.0

Gold binding site 9 out of 12 in 3hp3

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Gold binding site 9 out of 12 in the Crystal Structure of CXCL12


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 9 of Crystal Structure of CXCL12 within 5.0Å range:

Gold binding site 10 out of 12 in 3hp3

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Gold binding site 10 out of 12 in the Crystal Structure of CXCL12


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 10 of Crystal Structure of CXCL12 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Au109

b:0.6
occ:0.50
O H:HOH208 3.7 27.4 1.0

Reference:

J.W.Murphy, H.Yuan, Y.Kong, Y.Xiong, E.J.Lolis. Heterologous Quaternary Structure of CXCL12 and Its Relationship to the Cc Chemokine Family Proteins V. 78 1331 2009.
ISSN: ISSN 0887-3585
PubMed: 20077567
DOI: 10.1002/PROT.22666
Page generated: Sat Dec 12 01:53:33 2020

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