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Zinc in PDB 1yef: Structure of IGG2A Fab Fragment (D2.3) Complexed with Substrate Analogue

Protein crystallography data

The structure of Structure of IGG2A Fab Fragment (D2.3) Complexed with Substrate Analogue, PDB code: 1yef 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 / 2.00
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 78.200, 78.200, 158.700, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 24.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of IGG2A Fab Fragment (D2.3) Complexed with Substrate Analogue (pdb code 1yef). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of IGG2A Fab Fragment (D2.3) Complexed with Substrate Analogue, PDB code: 1yef:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1yef

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Zinc binding site 1 out of 8 in the Structure of IGG2A Fab Fragment (D2.3) Complexed with Substrate Analogue


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 (D2.3) Complexed with Substrate Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn215

b:28.2
occ:1.00
 O L:HOH637 1.7 37.9 1.0
O L:HOH604 2.4 23.9 1.0
O L:HOH645 2.6 49.4 1.0
O L:HOH581 3.7 32.6 1.0
O H:HOH287 4.0 49.2 1.0
O L:HOH608 4.4 34.5 1.0
O H:HOH256 4.6 50.7 1.0
CE L:LYS30 4.7 36.1 1.0
O H:HOH285 4.8 39.4 1.0
NZ L:LYS30 4.8 41.3 1.0

Zinc binding site 2 out of 8 in 1yef

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Zinc binding site 2 out of 8 in the Structure of IGG2A Fab Fragment (D2.3) Complexed with Substrate Analogue


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 (D2.3) Complexed with Substrate Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn216

b:49.2
occ:1.00
 O L:HOH556 1.8 49.7 1.0
O L:HOH589 2.0 24.8 1.0
O L:HOH555 2.7 10.0 1.0
ZN L:ZN218 3.6 23.5 1.0
O L:HOH642 3.6 36.9 1.0
O7 L:PNC551 3.7 44.8 1.0
N L:PHE94 3.7 18.9 1.0
CA L:HIS93 4.2 17.4 1.0
O L:THR92 4.3 17.6 1.0
CB L:PHE94 4.3 19.0 1.0
C L:HIS93 4.5 19.6 1.0
CA L:PHE94 4.6 19.3 1.0
O L:HOH644 4.7 32.7 1.0
C13 L:PNC551 4.7 40.9 1.0
O L:PHE94 4.8 22.0 1.0
ZN L:ZN222 5.0 54.2 1.0
CB L:HIS93 5.0 15.9 1.0

Zinc binding site 3 out of 8 in 1yef

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Zinc binding site 3 out of 8 in the Structure of IGG2A Fab Fragment (D2.3) Complexed with Substrate Analogue


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 (D2.3) Complexed with Substrate Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn217

b:25.4
occ:1.00
 O L:HOH597 1.5 51.2 1.0
O L:HOH592 1.6 50.5 1.0
OD1 H:ASP100C 2.1 32.2 1.0
NE2 L:HIS49 2.2 16.1 1.0
CG H:ASP100C 2.8 30.3 1.0
OD2 H:ASP100C 2.8 31.7 1.0
CE1 L:HIS49 3.1 14.5 1.0
O L:HOH636 3.2 45.6 1.0
CD2 L:HIS49 3.2 15.0 1.0
ND1 L:HIS49 4.2 16.2 1.0
N H:TYR100D 4.2 21.4 1.0
CB H:ASP100C 4.3 24.9 1.0
CG L:HIS49 4.3 15.1 1.0
O H:TYR100D 4.3 28.8 1.0
CB L:LYS53 4.3 24.1 1.0
CG L:LYS53 4.6 28.3 1.0
CA H:ASP100C 4.8 22.7 1.0
CD1 L:LEU50 4.9 19.0 1.0

Zinc binding site 4 out of 8 in 1yef

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Zinc binding site 4 out of 8 in the Structure of IGG2A Fab Fragment (D2.3) Complexed with Substrate Analogue


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 (D2.3) Complexed with Substrate Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn218

b:23.5
occ:1.00
 O L:HOH642 1.7 36.9 1.0
O L:HOH589 1.8 24.8 1.0
ND1 L:HIS93 2.4 19.3 1.0
O L:HOH621 3.2 34.3 1.0
CG L:HIS93 3.3 21.0 1.0
CE1 L:HIS93 3.4 20.6 1.0
CB L:HIS93 3.5 15.9 1.0
O L:HOH556 3.5 49.7 1.0
ZN L:ZN222 3.6 54.2 1.0
ZN L:ZN216 3.6 49.2 1.0
CA L:HIS93 3.9 17.4 1.0
CD2 L:HIS93 4.4 21.7 1.0
NE2 L:HIS93 4.4 22.2 1.0
O L:THR92 4.7 17.6 1.0
C L:HIS93 4.9 19.6 1.0
N L:HIS93 4.9 16.7 1.0
O L:HOH566 4.9 33.8 1.0
N L:PHE94 5.0 18.9 1.0

Zinc binding site 5 out of 8 in 1yef

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Zinc binding site 5 out of 8 in the Structure of IGG2A Fab Fragment (D2.3) Complexed with Substrate Analogue


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 (D2.3) Complexed with Substrate Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn219

b:25.5
occ:1.00
 O L:HOH587 2.0 18.4 1.0
OD2 L:ASP151 2.0 22.9 1.0
ND1 L:HIS189 2.3 25.4 1.0
CG L:ASP151 2.9 16.1 1.0
CE1 L:HIS189 3.3 28.1 1.0
CG L:HIS189 3.3 26.4 1.0
CB L:ASP151 3.3 17.8 1.0
ZN L:ZN220 3.3 27.8 1.0
CB L:HIS189 3.5 24.0 1.0
O L:HOH574 3.6 41.6 1.0
CA L:HIS189 3.7 23.8 1.0
O L:HOH646 3.9 33.6 1.0
O L:HOH615 3.9 42.4 1.0
OD1 L:ASP151 4.1 22.4 1.0
O L:ARG188 4.2 32.7 1.0
NE2 L:HIS189 4.3 31.7 1.0
CG2 L:ILE150 4.3 19.7 1.0
CD2 L:HIS189 4.4 26.9 1.0
O L:HOH605 4.4 21.3 1.0
O L:HOH606 4.5 36.7 1.0
N L:HIS189 4.6 24.9 1.0
CA L:ASP151 4.7 17.0 1.0
N L:ASN190 4.8 27.5 1.0
C L:ARG188 4.8 28.9 1.0
C L:HIS189 4.8 24.6 1.0
O L:ILE150 4.8 21.8 1.0
N L:ASP151 4.9 20.0 1.0
C L:ILE150 5.0 19.7 1.0
ZN L:ZN221 5.0 29.2 1.0

Zinc binding site 6 out of 8 in 1yef

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Zinc binding site 6 out of 8 in the Structure of IGG2A Fab Fragment (D2.3) Complexed with Substrate Analogue


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 (D2.3) Complexed with Substrate Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn220

b:27.8
occ:1.00
 O L:HOH615 1.7 42.4 1.0
O L:HOH587 1.8 18.4 1.0
O L:HOH606 2.3 36.7 1.0
ZN L:ZN219 3.3 25.5 1.0
ZN L:ZN221 3.4 29.2 1.0
O L:HOH646 3.6 33.6 1.0
O L:HOH605 4.0 21.3 1.0
CB L:ASP151 4.3 17.8 1.0
OG L:SER153 4.5 38.7 1.0
OD2 L:ASP151 4.7 22.9 1.0
O L:HOH574 4.7 41.6 1.0
O L:ASP151 4.9 18.9 1.0
ND1 L:HIS189 5.0 25.4 1.0

Zinc binding site 7 out of 8 in 1yef

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Zinc binding site 7 out of 8 in the Structure of IGG2A Fab Fragment (D2.3) Complexed with Substrate Analogue


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 (D2.3) Complexed with Substrate Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn221

b:29.2
occ:1.00
 O L:HOH605 1.6 21.3 1.0
O L:HOH606 1.7 36.7 1.0
O L:HOH615 3.3 42.4 1.0
ZN L:ZN220 3.4 27.8 1.0
O L:HOH574 3.8 41.6 1.0
O L:HOH587 4.7 18.4 1.0
ZN L:ZN219 5.0 25.5 1.0

Zinc binding site 8 out of 8 in 1yef

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Zinc binding site 8 out of 8 in the Structure of IGG2A Fab Fragment (D2.3) Complexed with Substrate Analogue


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of IGG2A Fab Fragment (D2.3) Complexed with Substrate Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn222

b:54.2
occ:1.00
 O L:HOH621 1.6 34.3 1.0
O L:HOH642 2.6 36.9 1.0
ZN L:ZN218 3.6 23.5 1.0
O L:HOH556 4.4 49.7 1.0
O L:HOH589 4.4 24.8 1.0
O L:HOH614 4.6 31.5 1.0
ZN L:ZN216 5.0 49.2 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: Wed Oct 16 20:52:58 2024

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