Atomistry » Zinc » PDB 1y8f-1yj6 » 1yej
Atomistry »
  Zinc »
    PDB 1y8f-1yj6 »
      1yej »

Zinc in PDB 1yej: Catalytic Antibody Complex

Protein crystallography data

The structure of Catalytic Antibody Complex, PDB code: 1yej 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 / 1.85
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 78.271, 78.271, 158.674, 90.00, 90.00, 120.00
R / Rfree (%) 21.2 / 24.6

Zinc Binding Sites:

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

Zinc binding site 1 out of 7 in 1yej

Go back to Zinc Binding Sites List in 1yej
Zinc binding site 1 out of 7 in the Catalytic Antibody Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Catalytic Antibody Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn601

b:30.1
occ:1.00
NZ L:LYS30 4.5 41.0 1.0
O L:HOH682 4.6 50.4 1.0

Zinc binding site 2 out of 7 in 1yej

Go back to Zinc Binding Sites List in 1yej
Zinc binding site 2 out of 7 in the Catalytic Antibody Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Catalytic Antibody Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn603

b:23.6
occ:1.00
O L:HOH647 1.9 42.8 1.0
OD1 H:ASP100C 2.1 24.8 1.0
NE2 L:HIS49 2.3 16.8 1.0
CE L:LYS53 2.8 37.0 1.0
CG H:ASP100C 2.9 27.4 1.0
NZ L:LYS53 3.0 42.9 1.0
OD2 H:ASP100C 3.0 27.0 1.0
CD2 L:HIS49 3.2 15.6 1.0
CE1 L:HIS49 3.3 16.1 1.0
CD L:LYS53 4.0 35.8 1.0
ND1 L:HIS49 4.3 16.3 1.0
CG L:HIS49 4.4 16.9 1.0
CB H:ASP100C 4.4 25.2 1.0
CB L:LYS53 4.4 23.1 1.0
N H:TYR100D 4.4 20.4 1.0
O H:TYR100D 4.6 24.4 1.0
CG L:LYS53 4.7 26.7 1.0
CA H:ASP100C 4.9 24.3 1.0
CD1 L:LEU50 4.9 19.3 1.0

Zinc binding site 3 out of 7 in 1yej

Go back to Zinc Binding Sites List in 1yej
Zinc binding site 3 out of 7 in the Catalytic Antibody Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Catalytic Antibody Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn604

b:25.2
occ:1.00
ND1 L:HIS93 2.2 18.6 1.0
O7 L:PNF551 2.2 56.3 1.0
O L:HOH691 2.8 40.7 1.0
CE1 L:HIS93 2.8 18.3 1.0
ZN L:ZN602 3.0 44.9 1.0
C17 L:PNF551 3.1 55.1 1.0
CG L:HIS93 3.4 17.7 1.0
O L:HOH696 3.5 47.6 1.0
O8 L:PNF551 3.6 59.5 1.0
CB L:HIS93 3.9 13.8 1.0
OE1 L:GLN27 4.0 50.5 1.0
NE2 L:HIS93 4.0 21.5 1.0
C16 L:PNF551 4.1 53.4 1.0
CA L:HIS93 4.3 14.3 1.0
CD2 L:HIS93 4.3 18.6 1.0
C15 L:PNF551 4.5 52.4 1.0
O L:THR92 4.6 15.3 1.0

Zinc binding site 4 out of 7 in 1yej

Go back to Zinc Binding Sites List in 1yej
Zinc binding site 4 out of 7 in the Catalytic Antibody Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Catalytic Antibody Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn605

b:24.2
occ:1.00
O L:HOH642 1.7 18.2 1.0
OD2 L:ASP151 1.9 23.2 1.0
O L:HOH657 2.1 26.2 1.0
ND1 L:HIS189 2.3 26.8 1.0
CG L:ASP151 2.9 17.6 1.0
CG L:HIS189 3.2 28.2 1.0
CE1 L:HIS189 3.2 26.6 1.0
CB L:ASP151 3.3 16.0 1.0
ZN L:ZN606 3.3 27.0 1.0
O L:HOH615 3.5 37.3 1.0
CB L:HIS189 3.5 25.7 1.0
O L:HOH658 3.6 28.9 1.0
CA L:HIS189 3.7 24.6 1.0
OD1 L:ASP151 4.0 20.6 1.0
NE2 L:HIS189 4.2 28.8 1.0
CD2 L:HIS189 4.3 30.2 1.0
CG2 L:ILE150 4.4 21.1 1.0
O L:ARG188 4.4 28.8 1.0
O L:HOH698 4.5 40.9 1.0
N L:HIS189 4.6 25.3 1.0
O L:HOH697 4.6 35.2 1.0
CA L:ASP151 4.7 17.3 1.0
N L:ASN190 4.7 26.5 1.0
C L:HIS189 4.8 23.2 1.0
C L:ARG188 4.8 28.4 1.0
O L:HOH629 4.8 21.9 1.0
O L:ILE150 4.9 19.9 1.0
ZN L:ZN607 5.0 29.4 1.0
N L:ASP151 5.0 19.5 1.0

Zinc binding site 5 out of 7 in 1yej

Go back to Zinc Binding Sites List in 1yej
Zinc binding site 5 out of 7 in the Catalytic Antibody Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Catalytic Antibody Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn602

b:44.9
occ:1.00
O L:HOH696 1.7 47.6 1.0
O L:HOH691 1.8 40.7 1.0
ZN L:ZN604 3.0 25.2 1.0
O7 L:PNF551 4.6 56.3 1.0
O L:HOH678 4.6 31.3 1.0
C17 L:PNF551 4.9 55.1 1.0
ND1 L:HIS93 4.9 18.6 1.0

Zinc binding site 6 out of 7 in 1yej

Go back to Zinc Binding Sites List in 1yej
Zinc binding site 6 out of 7 in the Catalytic Antibody Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Catalytic Antibody Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn606

b:27.0
occ:1.00
O L:HOH697 1.6 35.2 1.0
O L:HOH658 1.7 28.9 1.0
O L:HOH642 1.7 18.2 1.0
O L:HOH615 3.2 37.3 1.0
ZN L:ZN605 3.3 24.2 1.0
ZN L:ZN607 3.4 29.4 1.0
O L:HOH629 3.5 21.9 1.0
O L:HOH657 3.6 26.2 1.0
O L:HOH660 3.9 28.1 1.0
O L:HOH698 3.9 40.9 1.0
CB L:ASP151 4.4 16.0 1.0
OG L:SER153 4.6 33.0 1.0
OD2 L:ASP151 4.6 23.2 1.0
ND1 L:HIS189 4.9 26.8 1.0
O L:ASP151 5.0 19.9 1.0

Zinc binding site 7 out of 7 in 1yej

Go back to Zinc Binding Sites List in 1yej
Zinc binding site 7 out of 7 in the Catalytic Antibody Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Catalytic Antibody Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn607

b:29.4
occ:1.00
O L:HOH698 1.6 40.9 1.0
O L:HOH658 1.9 28.9 1.0
O L:HOH660 1.9 28.1 1.0
ZN L:ZN606 3.4 27.0 1.0
O L:HOH657 3.7 26.2 1.0
O L:HOH629 3.7 21.9 1.0
O L:HOH642 4.3 18.2 1.0
O L:HOH697 4.4 35.2 1.0
ZN L:ZN605 5.0 24.2 1.0

Reference:

B.Gigant, J.B.Charbonnier, Z.Eshhar, B.S.Green, M.Knossow. Crossreactivity, Efficiency and Catalytic Specificity of An Esterase-Like Antibody. J.Mol.Biol. V. 284 741 1998.
ISSN: ISSN 0022-2836
PubMed: 9826512
DOI: 10.1006/JMBI.1998.2198
Page generated: Wed Dec 16 03:14:20 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy