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Cadmium in PDB 1mnu: Unliganded Bactericidal Antibody Against Neisseria Meningitidis

Protein crystallography data

The structure of Unliganded Bactericidal Antibody Against Neisseria Meningitidis, PDB code: 1mnu was solved by J.Van Den Elsen, L.Vandeputte-Rutten, J.Kroon, P.Gros, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.617, 85.862, 87.133, 90.00, 122.69, 90.00
R / Rfree (%) 23.1 / 27

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Unliganded Bactericidal Antibody Against Neisseria Meningitidis (pdb code 1mnu). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Unliganded Bactericidal Antibody Against Neisseria Meningitidis, PDB code: 1mnu:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 1mnu

Go back to Cadmium Binding Sites List in 1mnu
Cadmium binding site 1 out of 3 in the Unliganded Bactericidal Antibody Against Neisseria Meningitidis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Unliganded Bactericidal Antibody Against Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cd220

b:37.9
occ:1.00
ND1 L:HIS98 2.5 18.5 1.0
O L:HOH316 2.6 12.3 1.0
CG L:HIS98 3.4 19.2 1.0
CE1 L:HIS98 3.4 20.0 1.0
CB L:HIS98 3.6 17.7 1.0
CA L:HIS98 4.0 17.7 1.0
NE2 L:GLN27 4.2 36.4 1.0
NE2 L:HIS98 4.5 22.2 1.0
CD2 L:HIS98 4.5 18.9 1.0
N L:VAL99 4.8 15.3 1.0
O L:THR97 4.9 21.6 1.0
C L:HIS98 5.0 16.6 1.0

Cadmium binding site 2 out of 3 in 1mnu

Go back to Cadmium Binding Sites List in 1mnu
Cadmium binding site 2 out of 3 in the Unliganded Bactericidal Antibody Against Neisseria Meningitidis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Unliganded Bactericidal Antibody Against Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cd221

b:40.7
occ:1.00
NE2 H:HIS172 2.5 14.5 1.0
ND2 L:ASN143 2.6 19.8 1.0
O H:HOH303 2.8 5.5 1.0
CG L:ASN143 3.3 19.0 1.0
CE1 H:HIS172 3.4 17.2 1.0
CD2 H:HIS172 3.4 15.6 1.0
OD1 L:ASN143 3.5 21.9 1.0
O H:HOH288 3.7 31.0 1.0
O L:HOH284 4.2 41.4 1.0
ND1 H:HIS172 4.5 17.5 1.0
CG H:HIS172 4.6 16.6 1.0
CB L:ASN143 4.6 18.0 1.0
OG L:SER179 4.7 19.5 1.0
OD2 L:ASP172 4.7 42.6 1.0
OD2 L:ASP175 4.8 40.8 1.0
CA H:GLY170 5.0 18.8 1.0

Cadmium binding site 3 out of 3 in 1mnu

Go back to Cadmium Binding Sites List in 1mnu
Cadmium binding site 3 out of 3 in the Unliganded Bactericidal Antibody Against Neisseria Meningitidis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Unliganded Bactericidal Antibody Against Neisseria Meningitidis within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cd222

b:21.1
occ:1.00
NE2 L:HIS194 2.4 4.5 1.0
OE2 L:GLU190 2.6 23.4 1.0
OE1 L:GLU190 2.6 27.9 1.0
O L:HOH317 2.6 2.0 1.0
CD L:GLU190 2.9 25.3 1.0
CE1 L:HIS194 3.3 11.8 1.0
CD2 L:HIS194 3.4 10.2 1.0
NE L:ARG193 4.0 17.3 1.0
NH1 L:ARG160 4.2 18.1 1.0
NH2 L:ARG160 4.3 26.9 1.0
CG L:GLU190 4.5 24.1 1.0
ND1 L:HIS194 4.5 8.9 1.0
CG L:HIS194 4.5 10.0 1.0
NH2 L:ARG193 4.5 15.6 1.0
CZ L:ARG193 4.8 17.4 1.0
CZ L:ARG160 4.8 20.0 1.0
CB L:ARG193 4.9 19.3 1.0
CD L:ARG193 4.9 17.9 1.0
O L:GLU190 5.0 20.9 1.0

Reference:

J.Van Den Elsen, L.Vandeputte-Rutten, J.Kroon, P.Gros. Bactericidal Antibody Recognition of Meningococcal Pora By Induced Fit. Comparison of Liganded and Unliganded Fab Structures. J.Biol.Chem. V. 274 1495 1999.
ISSN: ISSN 0021-9258
PubMed: 9880525
DOI: 10.1074/JBC.274.3.1495
Page generated: Wed Oct 28 09:54:50 2020
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