Zinc in PDB 2gjz: Structure of Catalytic Elimination Antibody 13G5 From A Crystal in Space Group P2(1)

The structure of Structure of Catalytic Elimination Antibody 13G5 From A Crystal in Space Group P2(1), PDB code: 2gjz was solved by E.W.Debler, I.A.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.209, 73.495, 130.475, 90.00, 96.33, 90.00
R / Rfree (%)	21.3 / 25

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

Binding sites:

The binding sites of Zinc atom in the Structure of Catalytic Elimination Antibody 13G5 From A Crystal in Space Group P2(1) (pdb code 2gjz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 11 binding sites of Zinc where determined in the Structure of Catalytic Elimination Antibody 13G5 From A Crystal in Space Group P2(1), PDB code: 2gjz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in the Structure of Catalytic Elimination Antibody 13G5 From A Crystal in Space Group P2(1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Catalytic Elimination Antibody 13G5 From A Crystal in Space Group P2(1) within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn213 b:97.7 occ:1.00 ND1 L:HIS27D 1.9 97.2 1.0 CE1 L:HIS27D 2.5 97.1 1.0 CG L:HIS27D 3.1 97.3 1.0 NE2 L:HIS27D 3.8 97.1 1.0 CB L:HIS27D 3.8 97.6 1.0 ND2 L:ASN28 4.0 0.4 1.0 CD2 L:HIS27D 4.1 97.3 1.0 CA L:HIS27D 4.7 97.6 1.0 CG L:ASN28 4.8 100.0 1.0

Zinc binding site 2 out of 11 in the Structure of Catalytic Elimination Antibody 13G5 From A Crystal in Space Group P2(1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Catalytic Elimination Antibody 13G5 From A Crystal in Space Group P2(1) within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn214 b:83.0 occ:1.00 OD2 L:ASP60 1.9 96.9 1.0 CG L:ASP60 2.7 95.9 1.0 OD1 L:ASP60 3.3 96.6 1.0 CB L:ASP60 3.8 95.4 1.0

Zinc binding site 3 out of 11 in the Structure of Catalytic Elimination Antibody 13G5 From A Crystal in Space Group P2(1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Catalytic Elimination Antibody 13G5 From A Crystal in Space Group P2(1) within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn215 b:0.2 occ:1.00 NE2 H:HIS172 2.0 97.3 1.0 ND2 L:ASN138 2.4 96.3 1.0 CE1 H:HIS172 2.5 96.8 1.0 O H:HOH232 2.8 65.8 1.0 OD1 L:ASN138 3.0 98.6 1.0 CG L:ASN138 3.0 94.0 1.0 CD2 H:HIS172 3.3 96.2 1.0 OD2 L:ASP167 3.5 0.4 1.0 ND1 H:HIS172 3.8 95.8 1.0 CG H:HIS172 4.2 95.1 1.0 OD2 L:ASP170 4.2 0.4 1.0 OG L:SER174 4.3 96.5 1.0 CB L:ASN138 4.4 92.0 1.0 OG1 L:THR172 4.4 93.5 1.0 CG L:ASP167 4.5 99.5 1.0 OD1 L:ASP170 4.6 0.1 1.0 CA L:ASN138 4.8 91.7 1.0 CG L:ASP170 4.8 99.7 1.0 N L:ASN138 4.9 91.8 1.0 CB L:ASP167 4.9 97.7 1.0

Zinc binding site 4 out of 11 in the Structure of Catalytic Elimination Antibody 13G5 From A Crystal in Space Group P2(1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Catalytic Elimination Antibody 13G5 From A Crystal in Space Group P2(1) within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn216 b:81.6 occ:1.00 OD2 L:ASP151 1.9 80.7 1.0 ND1 L:HIS189 1.9 93.4 1.0 O L:HOH222 2.5 58.8 1.0 CE1 L:HIS189 2.7 94.3 1.0 CG L:HIS189 3.0 93.8 1.0 CG L:ASP151 3.1 84.6 1.0 CB L:HIS189 3.5 93.6 1.0 CA L:HIS189 3.7 93.7 1.0 CB L:ASP151 3.7 87.4 1.0 O L:ARG188 3.8 92.9 1.0 NE2 L:HIS189 3.9 94.4 1.0 CD2 L:HIS189 4.0 92.0 1.0 OD1 L:ASP151 4.1 80.9 1.0 C L:ARG188 4.6 93.4 1.0 N L:HIS189 4.6 93.4 1.0 N L:ASN190 4.6 94.1 1.0 C L:HIS189 4.7 93.6 1.0

Zinc binding site 5 out of 11 in the Structure of Catalytic Elimination Antibody 13G5 From A Crystal in Space Group P2(1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Catalytic Elimination Antibody 13G5 From A Crystal in Space Group P2(1) within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn217 b:81.1 occ:1.00 ND1 L:HIS93 2.1 90.2 1.0 O L:HOH223 2.5 57.8 1.0 O L:HOH219 2.6 52.6 1.0 CE1 L:HIS93 2.8 89.8 1.0 CG L:HIS93 3.3 90.7 1.0 CB L:HIS93 3.9 91.1 1.0 NE2 L:HIS93 4.1 88.7 1.0 OE1 L:GLN27 4.3 95.0 1.0 CD2 L:HIS93 4.3 89.6 1.0 CA L:HIS93 4.5 91.1 1.0 CD1 L:LEU2 4.9 82.6 1.0

Zinc binding site 6 out of 11 in the Structure of Catalytic Elimination Antibody 13G5 From A Crystal in Space Group P2(1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Catalytic Elimination Antibody 13G5 From A Crystal in Space Group P2(1) within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn229 b:74.0 occ:1.00 NE2 H:HIS95 1.9 97.6 1.0 OD1 H:ASP35 2.1 90.2 1.0 OD2 H:ASP35 2.1 92.5 1.0 CG H:ASP35 2.4 91.9 1.0 CE1 H:HIS95 2.7 97.8 1.0 O H:HOH231 2.8 59.8 1.0 CD2 H:HIS95 3.0 97.1 1.0 CG2 H:VAL50 3.8 90.5 1.0 ND1 H:HIS95 3.9 96.8 1.0 CB H:ASP35 4.0 91.4 1.0 CB H:VAL50 4.0 91.2 1.0 NE1 H:TRP47 4.0 91.2 1.0 CG H:HIS95 4.0 95.9 1.0 CG H:PRO100B 4.2 0.3 1.0 CG1 H:VAL50 4.6 90.6 1.0 CE2 H:TRP47 4.7 91.7 1.0 CB H:PRO100B 4.8 99.9 1.0 CA H:ASP35 4.8 91.9 1.0 CZ2 H:TRP47 4.9 92.0 1.0 SD H:MET100E 4.9 97.6 1.0 CD1 H:TRP47 4.9 91.6 1.0 CG H:MET100E 5.0 96.2 1.0

Zinc binding site 7 out of 11 in the Structure of Catalytic Elimination Antibody 13G5 From A Crystal in Space Group P2(1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Catalytic Elimination Antibody 13G5 From A Crystal in Space Group P2(1) within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn230 b:86.5 occ:1.00 NE2 H:HIS102 2.3 95.8 1.0 CE1 H:HIS102 3.1 95.8 1.0 CD2 H:HIS102 3.3 94.1 1.0 OD1 H:ASP101 3.9 98.2 1.0 OD2 H:ASP101 4.0 95.5 1.0 ND1 H:HIS102 4.3 95.2 1.0 CG H:ASP101 4.3 95.6 1.0 CG H:HIS102 4.3 94.2 1.0 CZ L:PHE55 5.0 96.7 1.0

Zinc binding site 8 out of 11 in the Structure of Catalytic Elimination Antibody 13G5 From A Crystal in Space Group P2(1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Catalytic Elimination Antibody 13G5 From A Crystal in Space Group P2(1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn213 b:57.4 occ:1.00 OD2 A:ASP151 1.6 79.8 1.0 ND1 A:HIS189 2.0 94.4 1.0 O A:HOH214 2.4 38.0 1.0 CG A:ASP151 2.8 86.5 1.0 CE1 A:HIS189 2.9 94.0 1.0 CG A:HIS189 3.1 93.3 1.0 CB A:HIS189 3.5 93.0 1.0 CB A:ASP151 3.6 86.8 1.0 OD1 A:ASP151 3.8 87.1 1.0 CA A:HIS189 3.9 93.3 1.0 O A:ARG188 3.9 92.4 1.0 NE2 A:HIS189 4.0 94.6 1.0 CD2 A:HIS189 4.2 91.4 1.0 C A:ARG188 4.7 93.5 1.0 N A:HIS189 4.7 93.3 1.0 N A:ASN190 4.8 94.2 1.0 C A:HIS189 5.0 93.7 1.0 CA A:ASP151 5.0 87.8 1.0

Zinc binding site 9 out of 11 in the Structure of Catalytic Elimination Antibody 13G5 From A Crystal in Space Group P2(1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Catalytic Elimination Antibody 13G5 From A Crystal in Space Group P2(1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn229 b:95.5 occ:1.00 NE2 B:HIS172 2.2 97.2 1.0 ND2 A:ASN138 2.7 97.2 1.0 OD2 A:ASP167 2.9 0.3 1.0 CE1 B:HIS172 2.9 97.0 1.0 O A:HOH222 3.2 71.4 1.0 CD2 B:HIS172 3.4 96.3 1.0 CG A:ASN138 3.6 94.3 1.0 OD1 A:ASN138 3.7 98.2 1.0 CG A:ASP167 3.9 99.8 1.0 ND1 B:HIS172 4.1 96.2 1.0 OD2 A:ASP170 4.1 0.5 1.0 CG B:HIS172 4.4 95.4 1.0 CB A:ASP167 4.4 97.7 1.0 OD1 A:ASP170 4.5 0.1 1.0 OG1 A:THR172 4.6 94.0 1.0 CG A:ASP170 4.7 99.8 1.0 OG A:SER174 4.7 96.6 1.0 OD1 A:ASP167 4.8 0.9 1.0 CB A:ASN138 4.9 92.0 1.0

Zinc binding site 10 out of 11 in the Structure of Catalytic Elimination Antibody 13G5 From A Crystal in Space Group P2(1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Catalytic Elimination Antibody 13G5 From A Crystal in Space Group P2(1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn230 b:75.2 occ:1.00 NE2 B:HIS95 2.2 97.5 1.0 OD1 B:ASP35 2.2 90.4 1.0 OD2 B:ASP35 2.3 92.9 1.0 O B:HOH240 2.5 55.5 1.0 CG B:ASP35 2.6 92.2 1.0 CE1 B:HIS95 3.0 97.6 1.0 CD2 B:HIS95 3.2 96.6 1.0 NE1 B:TRP47 3.9 91.3 1.0 CG2 B:VAL50 4.0 90.4 1.0 CB B:VAL50 4.0 91.0 1.0 ND1 B:HIS95 4.1 96.2 1.0 CB B:ASP35 4.1 91.5 1.0 CG B:HIS95 4.3 95.6 1.0 CE2 B:TRP47 4.6 91.7 1.0 CG B:PRO100B 4.6 0.0 1.0 CG1 B:VAL50 4.6 90.5 1.0 CZ2 B:TRP47 4.7 91.9 1.0 CD1 B:TRP47 4.8 91.5 1.0 CA B:ASP35 5.0 91.9 1.0 SD B:MET100E 5.0 97.8 1.0

R.Muller, E.W.Debler, M.Steinmann, F.P.Seebeck, I.A.Wilson, D.Hilvert. Bifunctional Catalysis of Proton Transfer at An Antibody Active Site. J.Am.Chem.Soc. V. 129 460 2007.
ISSN: ISSN 0002-7863
PubMed: 17226987
DOI: 10.1021/JA066578B