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Zinc in PDB 3if1: Crystal Structure of 237MAB in Complex with A Galnac

Protein crystallography data

The structure of Crystal Structure of 237MAB in Complex with A Galnac, PDB code: 3if1 was solved by C.L.Brooks, S.V.Evans, S.N.Borisova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.93 / 2.39
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 279.350, 38.420, 95.990, 90.00, 109.11, 90.00
R / Rfree (%) 22.4 / 28.5

Other elements in 3if1:

The structure of Crystal Structure of 237MAB in Complex with A Galnac also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of 237MAB in Complex with A Galnac (pdb code 3if1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of 237MAB in Complex with A Galnac, PDB code: 3if1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 3if1

Go back to Zinc Binding Sites List in 3if1
Zinc binding site 1 out of 5 in the Crystal Structure of 237MAB in Complex with A Galnac


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of 237MAB in Complex with A Galnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn213

b:42.8
occ:1.00
NE2 A:HIS34 2.1 31.7 1.0
O B:HOH225 2.3 35.1 1.0
O A:HOH218 2.4 17.1 1.0
O A:HOH229 2.6 24.1 1.0
CE1 A:HIS34 2.7 29.4 1.0
CD2 A:HIS34 3.4 27.2 1.0
O B:HOH371 3.6 43.6 1.0
OG A:SER91 3.8 35.2 1.0
ND1 A:HIS34 3.9 30.1 1.0
CB B:ARG98 4.0 33.0 1.0
O B:ARG98 4.2 28.9 1.0
CD2 A:TYR32 4.2 23.4 1.0
CG A:HIS34 4.3 28.0 1.0
CG B:ARG98 4.6 38.4 1.0
O A:HOH223 4.6 32.0 1.0
CB A:TYR32 4.7 20.7 1.0
CB A:TYR49 4.7 28.5 1.0
N B:ARG98 4.7 32.0 1.0
CA B:ARG98 4.7 32.1 1.0
C B:ARG98 4.9 28.7 1.0
CG A:TYR32 4.9 20.7 1.0

Zinc binding site 2 out of 5 in 3if1

Go back to Zinc Binding Sites List in 3if1
Zinc binding site 2 out of 5 in the Crystal Structure of 237MAB in Complex with A Galnac


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of 237MAB in Complex with A Galnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn215

b:42.1
occ:1.00
NE2 A:HIS189 2.2 29.0 1.0
OE1 A:GLU185 2.5 40.9 1.0
OE2 A:GLU185 2.5 42.3 1.0
O A:HOH259 2.6 33.1 1.0
CD A:GLU185 2.8 41.4 1.0
CD2 A:HIS189 3.1 30.7 1.0
CE1 A:HIS189 3.2 35.1 1.0
NH1 A:ARG155 4.1 53.8 1.0
ND1 A:HIS189 4.3 33.0 1.0
CG A:HIS189 4.3 30.8 1.0
CG A:GLU185 4.3 35.9 1.0
NE A:ARG188 4.4 40.8 1.0
O A:GLU185 4.6 30.9 1.0
CB A:ARG188 4.8 30.6 1.0
NH1 A:ARG188 4.9 39.1 1.0
NH2 A:ARG155 5.0 36.8 1.0

Zinc binding site 3 out of 5 in 3if1

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Zinc binding site 3 out of 5 in the Crystal Structure of 237MAB in Complex with A Galnac


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of 237MAB in Complex with A Galnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn222

b:39.8
occ:1.00
O A:HOH243 3.0 25.3 1.0
O A:HOH234 3.2 17.3 1.0
MG A:MG214 3.3 19.4 1.0
N A:ILE2 3.4 22.7 1.0
OE1 A:GLN3 3.5 52.4 1.0
O A:HOH262 3.6 32.3 1.0
O A:HOH303 3.9 24.2 1.0
NE2 A:GLN3 4.2 48.0 1.0
CA A:ILE2 4.2 36.2 1.0
CD A:GLN3 4.2 38.8 1.0
NE2 A:GLN27 4.7 28.4 1.0
O A:HOH282 4.9 44.5 1.0

Zinc binding site 4 out of 5 in 3if1

Go back to Zinc Binding Sites List in 3if1
Zinc binding site 4 out of 5 in the Crystal Structure of 237MAB in Complex with A Galnac


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of 237MAB in Complex with A Galnac within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn218

b:30.2
occ:1.00
O C:HOH238 2.2 24.7 1.0
OE2 C:GLU123 2.4 30.3 1.0
OE1 C:GLU123 2.5 41.6 1.0
O C:HOH221 2.7 18.0 1.0
CD C:GLU123 2.8 32.0 1.0
O D:HOH370 4.0 45.9 1.0
OG1 C:THR126 4.2 33.6 1.0
CG C:GLU123 4.3 32.0 1.0
O C:HOH263 4.4 28.0 1.0
O C:HOH383 4.7 35.5 1.0
CA C:GLU123 5.0 26.2 1.0
CB C:GLU123 5.0 28.8 1.0
O C:GLU123 5.0 26.8 1.0

Zinc binding site 5 out of 5 in 3if1

Go back to Zinc Binding Sites List in 3if1
Zinc binding site 5 out of 5 in the Crystal Structure of 237MAB in Complex with A Galnac


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of 237MAB in Complex with A Galnac within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn221

b:32.9
occ:1.00
OD1 A:ASP143 2.1 33.2 1.0
ND1 D:HIS55 2.2 22.9 1.0
O A:HOH240 2.5 30.7 1.0
CG A:ASP143 2.7 33.3 1.0
OD2 A:ASP143 2.8 35.1 1.0
CG D:HIS55 3.1 31.0 1.0
CE1 D:HIS55 3.3 24.0 1.0
CB D:HIS55 3.3 25.1 1.0
CB A:ASP143 4.2 35.5 1.0
O D:HOH414 4.2 34.0 1.0
CD2 D:HIS55 4.3 30.3 1.0
NZ A:LYS142 4.3 41.6 1.0
NE2 D:HIS55 4.3 32.3 1.0
CE A:LYS142 4.3 56.3 1.0
O A:HOH245 4.4 24.8 1.0
CA D:HIS55 4.8 31.2 1.0
CG A:LYS142 5.0 32.2 1.0

Reference:

C.L.Brooks, A.Schietinger, S.N.Borisova, P.Kufer, M.Okon, T.Hirama, C.R.Mackenzie, L.X.Wang, H.Schreiber, S.V.Evans. Antibody Recognition of A Unique Tumor-Specific Glycopeptide Antigen. Proc.Natl.Acad.Sci.Usa V. 107 10056 2010.
ISSN: ISSN 0027-8424
PubMed: 20479270
DOI: 10.1073/PNAS.0915176107
Page generated: Wed Dec 16 04:26:16 2020

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