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Zinc in PDB 1yeh: Structure of IGG2A Fab Fragment

Protein crystallography data

The structure of Structure of IGG2A Fab Fragment, PDB code: 1yeh was solved by B.Gigant, M.Knossow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.00 / 2.55
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 78.470, 78.470, 158.920, 90.00, 90.00, 120.00
R / Rfree (%) 18.1 / 23.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of IGG2A Fab Fragment (pdb code 1yeh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Structure of IGG2A Fab Fragment, PDB code: 1yeh:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 1yeh

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Zinc binding site 1 out of 7 in the Structure of IGG2A Fab Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of IGG2A Fab Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn215

b:37.2
occ:1.00
O L:HOH270 1.7 22.1 1.0
O L:HOH271 1.7 10.0 1.0
ZN L:ZN221 3.5 36.5 1.0
ZN L:ZN219 3.6 31.8 1.0
O L:ARG188 3.7 30.5 1.0
OD2 L:ASP151 3.9 19.3 1.0
O L:HOH272 4.0 20.7 1.0
O L:HOH256 4.2 10.0 1.0
O L:HOH273 4.4 22.2 1.0
ND2 L:ASN190 4.5 54.3 1.0
O L:HOH279 4.5 33.3 1.0
ZN L:ZN220 4.8 26.5 1.0
CG L:ASP151 4.8 13.9 1.0
OD1 L:ASN190 4.9 53.6 1.0
C L:ARG188 4.9 27.4 1.0

Zinc binding site 2 out of 7 in 1yeh

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Zinc binding site 2 out of 7 in the Structure of IGG2A Fab Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of IGG2A Fab Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn216

b:30.9
occ:1.00
O L:HOH285 1.5 60.1 1.0
O L:HOH255 2.2 22.5 1.0
ZN L:ZN218 3.6 22.4 1.0
O L:HOH291 4.3 10.0 1.0
O L:HOH290 4.5 52.9 1.0

Zinc binding site 3 out of 7 in 1yeh

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Zinc binding site 3 out of 7 in the Structure of IGG2A Fab Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of IGG2A Fab Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn217

b:27.5
occ:1.00
O H:HOH251 1.6 60.5 1.0
O L:HOH287 1.6 34.1 1.0
O H:HOH255 2.0 47.1 1.0
NE2 L:HIS49 2.5 11.9 1.0
OD1 H:ASP100C 2.5 35.1 1.0
OD2 H:ASP100C 2.8 30.3 1.0
CG H:ASP100C 2.9 28.2 1.0
CE1 L:HIS49 3.3 11.5 1.0
CD2 L:HIS49 3.4 12.1 1.0
N H:TYR100D 4.3 19.6 1.0
CB L:LYS53 4.3 19.0 1.0
CB H:ASP100C 4.4 27.0 1.0
ND1 L:HIS49 4.4 15.3 1.0
O H:TYR100D 4.4 28.7 1.0
CG L:HIS49 4.5 11.9 1.0
CG L:LYS53 4.6 25.9 1.0
CA H:ASP100C 4.9 20.0 1.0
CD1 L:LEU50 4.9 9.2 1.0

Zinc binding site 4 out of 7 in 1yeh

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Zinc binding site 4 out of 7 in the Structure of IGG2A Fab Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of IGG2A Fab Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn218

b:22.4
occ:1.00
O L:HOH255 1.6 22.5 1.0
O L:HOH291 2.1 10.0 1.0
ND1 L:HIS93 2.5 19.2 1.0
CG L:HIS93 3.3 19.5 1.0
CB L:HIS93 3.4 16.1 1.0
CE1 L:HIS93 3.5 19.3 1.0
ZN L:ZN216 3.6 30.9 1.0
CA L:HIS93 3.9 14.8 1.0
O L:HOH235 4.3 28.3 1.0
CD2 L:HIS93 4.4 22.4 1.0
NE2 L:HIS93 4.5 21.0 1.0
N L:PHE94 4.7 19.3 1.0
O L:THR92 4.7 16.7 1.0
C L:HIS93 4.9 17.4 1.0
N L:HIS93 4.9 17.0 1.0

Zinc binding site 5 out of 7 in 1yeh

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Zinc binding site 5 out of 7 in the Structure of IGG2A Fab Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of IGG2A Fab Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn219

b:31.8
occ:1.00
O L:HOH256 1.7 10.0 1.0
OD2 L:ASP151 1.9 19.3 1.0
O L:HOH270 2.0 22.1 1.0
ND1 L:HIS189 2.5 30.7 1.0
CG L:ASP151 3.0 13.9 1.0
CG L:HIS189 3.2 31.5 1.0
CE1 L:HIS189 3.3 32.4 1.0
ZN L:ZN220 3.4 26.5 1.0
CB L:HIS189 3.5 27.8 1.0
CB L:ASP151 3.5 10.5 1.0
CA L:HIS189 3.6 27.0 1.0
O L:HOH279 3.6 33.3 1.0
O L:HOH229 3.6 28.6 1.0
ZN L:ZN215 3.6 37.2 1.0
O L:ARG188 3.9 30.5 1.0
OD1 L:ASP151 4.0 16.2 1.0
O L:HOH272 4.2 20.7 1.0
CD2 L:HIS189 4.2 35.2 1.0
NE2 L:HIS189 4.2 37.5 1.0
CG2 L:ILE150 4.4 15.4 1.0
N L:HIS189 4.4 28.1 1.0
O L:HOH271 4.5 10.0 1.0
C L:ARG188 4.5 27.4 1.0
C L:HIS189 4.7 27.1 1.0
N L:ASN190 4.7 29.6 1.0
O L:HOH281 4.8 61.9 1.0
O L:ILE150 4.8 20.2 1.0
CA L:ASP151 4.9 13.2 1.0
O L:HOH242 4.9 19.1 1.0

Zinc binding site 6 out of 7 in 1yeh

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Zinc binding site 6 out of 7 in the Structure of IGG2A Fab Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of IGG2A Fab Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn220

b:26.5
occ:1.00
O L:HOH281 1.6 61.9 1.0
O L:HOH279 1.8 33.3 1.0
O L:HOH256 1.8 10.0 1.0
O L:HOH272 1.8 20.7 1.0
O L:HOH229 3.2 28.6 1.0
O L:HOH242 3.3 19.1 1.0
ZN L:ZN219 3.4 31.8 1.0
ZN L:ZN221 3.5 36.5 1.0
O L:HOH270 3.8 22.1 1.0
O L:HOH271 4.3 10.0 1.0
O L:HOH273 4.3 22.2 1.0
CB L:ASP151 4.3 10.5 1.0
OD2 L:ASP151 4.5 19.3 1.0
OG L:SER153 4.6 35.2 1.0
ZN L:ZN215 4.8 37.2 1.0
O L:ASP151 4.9 19.2 1.0
CG L:ASP151 4.9 13.9 1.0
O L:ILE150 5.0 20.2 1.0

Zinc binding site 7 out of 7 in 1yeh

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Zinc binding site 7 out of 7 in the Structure of IGG2A Fab Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of IGG2A Fab Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn221

b:36.5
occ:1.00
O L:HOH273 1.7 22.2 1.0
O L:HOH272 1.7 20.7 1.0
O L:HOH271 1.9 10.0 1.0
O L:HOH242 3.5 19.1 1.0
ZN L:ZN215 3.5 37.2 1.0
ZN L:ZN220 3.5 26.5 1.0
O L:HOH279 3.7 33.3 1.0
O L:HOH270 4.0 22.1 1.0
O L:HOH256 4.4 10.0 1.0
O L:HOH281 4.5 61.9 1.0

Reference:

B.Gigant, J.B.Charbonnier, Z.Eshhar, B.S.Green, M.Knossow. X-Ray Structures of A Hydrolytic Antibody and of Complexes Elucidate Catalytic Pathway From Substrate Binding and Transition State Stabilization Through Water Attack and Product Release. Proc.Natl.Acad.Sci.Usa V. 94 7857 1997.
ISSN: ISSN 0027-8424
PubMed: 9223277
DOI: 10.1073/PNAS.94.15.7857
Page generated: Sat Sep 26 00:31:47 2020
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