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Zinc in PDB 4p2y: Crystal Structure of the Human Rage Ectodomain (Fragment VC1C2) in Complex with Mouse S100A6

Protein crystallography data

The structure of Crystal Structure of the Human Rage Ectodomain (Fragment VC1C2) in Complex with Mouse S100A6, PDB code: 4p2y was solved by L.Yatime, G.R.Andersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.24 / 2.30
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 76.780, 113.390, 140.320, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 20.7

Other elements in 4p2y:

The structure of Crystal Structure of the Human Rage Ectodomain (Fragment VC1C2) in Complex with Mouse S100A6 also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms
Calcium (Ca) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Human Rage Ectodomain (Fragment VC1C2) in Complex with Mouse S100A6 (pdb code 4p2y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the Human Rage Ectodomain (Fragment VC1C2) in Complex with Mouse S100A6, PDB code: 4p2y:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4p2y

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Zinc binding site 1 out of 6 in the Crystal Structure of the Human Rage Ectodomain (Fragment VC1C2) in Complex with Mouse S100A6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Human Rage Ectodomain (Fragment VC1C2) in Complex with Mouse S100A6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:38.9
occ:1.00
OE2 A:GLU182 2.0 39.6 1.0
ND1 A:HIS180 2.0 44.5 1.0
CE1 A:HIS180 2.9 44.6 1.0
CD A:GLU182 2.9 45.2 1.0
CG A:HIS180 3.1 45.8 1.0
OE1 A:GLU182 3.2 41.8 1.0
CB A:HIS180 3.5 34.3 1.0
NH1 A:ARG178 4.0 78.0 1.0
NE2 A:HIS180 4.1 50.3 1.0
O A:HOH1142 4.1 45.3 1.0
CD2 A:HIS180 4.2 49.5 1.0
CA A:HIS180 4.2 31.6 1.0
CG A:GLU182 4.3 44.4 1.0
NH2 A:ARG178 4.5 77.8 1.0
CZ A:ARG178 4.7 73.8 1.0
CD A:PRO181 4.9 38.0 1.0

Zinc binding site 2 out of 6 in 4p2y

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Zinc binding site 2 out of 6 in the Crystal Structure of the Human Rage Ectodomain (Fragment VC1C2) in Complex with Mouse S100A6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Human Rage Ectodomain (Fragment VC1C2) in Complex with Mouse S100A6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:38.5
occ:1.00
OD2 A:ASP160 2.0 42.2 1.0
OD2 A:ASP201 2.0 37.6 1.0
CL A:CL1007 2.1 36.2 1.0
CL A:CL1008 2.3 61.5 1.0
CG A:ASP201 2.9 39.0 1.0
CG A:ASP160 2.9 35.5 1.0
CB A:ASP201 3.1 37.7 1.0
OD1 A:ASP160 3.3 30.3 1.0
O A:HOH1107 3.8 45.1 1.0
OD1 A:ASP201 4.1 39.0 1.0
O B:HOH201 4.2 56.8 1.0
CB A:ASP160 4.3 33.6 1.0
O A:HOH1117 4.3 33.4 1.0
CA A:PRO204 4.6 33.2 1.0
CA A:ASP201 4.6 43.0 1.0
CB A:PRO204 4.9 36.6 1.0
CD1 A:LEU159 4.9 30.3 1.0

Zinc binding site 3 out of 6 in 4p2y

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Zinc binding site 3 out of 6 in the Crystal Structure of the Human Rage Ectodomain (Fragment VC1C2) in Complex with Mouse S100A6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Human Rage Ectodomain (Fragment VC1C2) in Complex with Mouse S100A6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:91.6
occ:1.00
ND1 A:HIS217 2.0 48.1 1.0
O A:HOH1144 2.1 54.8 1.0
CE1 A:HIS217 2.4 47.0 1.0
CG A:HIS217 3.4 43.2 1.0
NE2 A:HIS217 3.7 41.9 1.0
O A:HOH1141 3.9 29.2 1.0
CB A:HIS217 4.1 35.6 1.0
CD2 A:HIS217 4.2 42.5 1.0
CG A:PRO215 4.8 38.7 1.0
CA A:HIS217 4.8 38.6 1.0
O A:ARG216 4.9 40.3 1.0
O A:HOH1104 4.9 59.1 1.0

Zinc binding site 4 out of 6 in 4p2y

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Zinc binding site 4 out of 6 in the Crystal Structure of the Human Rage Ectodomain (Fragment VC1C2) in Complex with Mouse S100A6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Human Rage Ectodomain (Fragment VC1C2) in Complex with Mouse S100A6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1004

b:58.8
occ:1.00
ND1 A:HIS270 2.0 47.6 1.0
CL A:CL1009 2.4 75.8 1.0
CE1 A:HIS270 3.0 47.8 1.0
CG A:HIS270 3.0 41.9 1.0
CB A:HIS270 3.4 39.7 1.0
O A:LEU280 4.0 58.7 1.0
O A:HOH1113 4.1 44.5 1.0
NE2 A:HIS270 4.1 55.8 1.0
CD2 A:HIS270 4.2 51.4 1.0
CA A:HIS270 4.3 49.2 1.0
CG A:PRO282 4.8 62.2 1.0
CD A:PRO282 4.9 61.4 1.0
N A:PRO282 5.0 60.5 1.0

Zinc binding site 5 out of 6 in 4p2y

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Zinc binding site 5 out of 6 in the Crystal Structure of the Human Rage Ectodomain (Fragment VC1C2) in Complex with Mouse S100A6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Human Rage Ectodomain (Fragment VC1C2) in Complex with Mouse S100A6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn101

b:33.8
occ:1.00
OE1 A:GLU132 2.0 34.6 1.0
NE2 B:HIS17 2.0 39.0 1.0
ND1 B:HIS27 2.0 35.2 1.0
CL A:CL1006 2.1 31.5 1.0
CD A:GLU132 2.8 32.5 1.0
CE1 B:HIS27 2.9 26.3 1.0
OE2 A:GLU132 3.0 33.2 1.0
CD2 B:HIS17 3.0 28.3 1.0
CE1 B:HIS17 3.0 31.7 1.0
CG B:HIS27 3.1 35.9 1.0
CB B:HIS27 3.6 32.5 1.0
NE2 B:HIS27 4.0 33.2 1.0
ND1 B:HIS17 4.1 28.1 1.0
CG B:HIS17 4.1 29.8 1.0
CD2 B:HIS27 4.2 31.1 1.0
CG A:GLU132 4.2 26.3 1.0
O A:HOH1167 4.3 34.1 1.0
CA B:HIS27 4.4 32.5 1.0
NH2 A:ARG228 4.7 30.4 1.0
CE2 B:PHE16 4.7 33.8 1.0
CG A:TRP230 4.8 37.7 1.0
CD2 A:TRP230 4.9 37.1 1.0
CB A:TRP230 4.9 35.8 1.0
NE A:ARG228 4.9 32.2 1.0
CB A:GLU132 4.9 25.2 1.0
CE3 A:TRP230 4.9 37.8 1.0
CD2 B:PHE16 5.0 26.5 1.0

Zinc binding site 6 out of 6 in 4p2y

Go back to Zinc Binding Sites List in 4p2y
Zinc binding site 6 out of 6 in the Crystal Structure of the Human Rage Ectodomain (Fragment VC1C2) in Complex with Mouse S100A6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Human Rage Ectodomain (Fragment VC1C2) in Complex with Mouse S100A6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn105

b:54.3
occ:1.00
SG B:CYS3 2.3 50.0 1.0
CB B:CYS3 3.4 62.2 1.0
CA B:CYS3 4.0 65.1 1.0
CD B:PRO4 4.1 66.8 1.0
O B:HOH202 4.2 46.1 1.0
N B:PRO4 4.6 62.7 1.0
C B:CYS3 4.6 61.6 1.0
CG B:LEU5 4.7 49.9 1.0
CG B:PRO4 4.7 65.4 1.0
CD1 B:LEU5 4.8 49.3 1.0
CB B:LEU5 4.8 46.4 1.0
N B:LEU5 4.9 48.0 1.0

Reference:

L.Yatime, C.Betzer, S.Sirotkina, P.H.Jensen, G.R.Andersen. The Structure of the Rage:S100A6 Complex Reveals A New Mode of Homodimerization For S100 Proteins To Be Published.
Page generated: Wed Dec 16 05:39:56 2020

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