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Chlorine in PDB 3vty: Crystal Structure of Mama

Protein crystallography data

The structure of Crystal Structure of Mama, PDB code: 3vty was solved by N.Zeytuni, D.Baran, G.Davidov, R.Zarivach, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.99 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.701, 101.315, 139.553, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 21.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Mama (pdb code 3vty). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Mama, PDB code: 3vty:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 3vty

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Chlorine binding site 1 out of 6 in the Crystal Structure of Mama


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Mama within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:24.9
occ:1.00
 O A:HOH521 2.9 36.1 1.0
N A:LYS164 3.3 21.4 1.0
N A:ASP163 3.4 21.8 1.0
C A:GLU161 3.4 21.9 1.0
CA A:GLU161 3.5 23.1 1.0
CB A:GLU161 3.6 23.8 1.0
O A:GLU161 3.7 18.9 1.0
CB A:ASP163 3.7 23.4 1.0
N A:HIS162 3.8 21.5 1.0
CA A:ASP163 3.8 22.1 1.0
C A:ASP163 4.0 20.9 1.0
CG A:LYS164 4.0 25.2 1.0
OD2 A:ASP163 4.1 27.7 1.0
O A:HOH475 4.1 29.9 1.0
CB A:LYS164 4.3 21.5 1.0
C A:HIS162 4.3 20.5 1.0
CA A:LYS164 4.4 20.7 1.0
CG A:ASP163 4.4 24.7 1.0
CG A:GLU161 4.4 28.6 1.0
CD A:LYS164 4.5 28.8 1.0
CA A:HIS162 4.7 21.4 1.0
CE A:LYS164 4.7 32.3 1.0
N A:GLU161 4.8 22.4 1.0
O A:GLY160 5.0 24.4 1.0

Chlorine binding site 2 out of 6 in 3vty

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Chlorine binding site 2 out of 6 in the Crystal Structure of Mama


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Mama within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:15.4
occ:1.00
 OD1 C:ASN142 3.2 18.1 1.0
N B:ALA112 3.2 11.2 1.0
O C:HOH403 3.2 7.6 1.0
O B:HOH500 3.3 27.9 1.0
CB B:ALA112 3.6 11.8 1.0
CG C:ASN142 3.6 15.5 1.0
CB C:ASN142 3.7 15.5 1.0
CA B:ALA112 3.9 12.1 1.0
CB C:ALA112 3.9 8.2 1.0
N B:GLU113 3.9 11.4 1.0
C B:SER111 4.1 11.6 1.0
O C:HOH423 4.2 14.8 1.0
CA B:SER111 4.2 11.4 1.0
O B:THR110 4.4 14.3 1.0
C B:ALA112 4.4 11.4 1.0
OG B:SER111 4.7 8.7 1.0
ND2 C:ASN142 4.7 19.2 1.0
O B:HOH509 4.8 36.3 1.0
CB B:GLU113 4.9 12.8 1.0
N C:GLU113 4.9 8.3 1.0
CE1 C:TYR145 4.9 10.4 1.0
CD1 C:TYR145 5.0 9.3 1.0
O B:HOH496 5.0 20.6 1.0
CA C:ALA112 5.0 9.1 1.0

Chlorine binding site 3 out of 6 in 3vty

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Chlorine binding site 3 out of 6 in the Crystal Structure of Mama


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Mama within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl302

b:29.6
occ:1.00
 N B:LYS164 3.3 22.7 1.0
C B:GLU161 3.3 27.5 1.0
CA B:GLU161 3.4 28.9 1.0
N B:ASP163 3.5 24.5 1.0
O B:HOH476 3.5 36.3 1.0
CB B:GLU161 3.5 29.3 1.0
O B:GLU161 3.6 26.5 1.0
N B:HIS162 3.7 26.5 1.0
CB B:ASP163 3.7 27.7 1.0
CG B:LYS164 3.9 27.8 1.0
CA B:ASP163 3.9 26.0 1.0
CB B:LYS164 4.0 23.4 1.0
O B:HOH491 4.0 47.1 1.0
C B:ASP163 4.1 23.7 1.0
CD B:LYS164 4.2 34.6 1.0
CA B:LYS164 4.2 22.8 1.0
C B:HIS162 4.4 25.9 1.0
CG B:GLU161 4.5 33.8 1.0
CA B:HIS162 4.6 26.9 1.0
CG B:ASP163 4.6 32.0 1.0
N B:GLU161 4.8 29.0 1.0
OD2 B:ASP163 4.9 39.1 1.0

Chlorine binding site 4 out of 6 in 3vty

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Chlorine binding site 4 out of 6 in the Crystal Structure of Mama


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Mama within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl301

b:11.3
occ:1.00
 O C:HOH471 3.1 21.5 1.0
O C:HOH473 3.3 22.6 1.0
N C:ASP163 3.4 10.6 1.0
N C:LYS164 3.4 12.0 1.0
C C:GLU161 3.4 10.1 1.0
CA C:GLU161 3.5 9.1 1.0
CB C:ASP163 3.5 13.4 1.0
CB C:GLU161 3.6 11.3 1.0
O C:GLU161 3.7 10.4 1.0
N C:HIS162 3.8 9.2 1.0
CA C:ASP163 3.8 12.1 1.0
CG C:LYS164 3.8 14.8 1.0
C C:ASP163 4.1 11.7 1.0
CB C:LYS164 4.1 11.7 1.0
CD C:LYS164 4.3 20.8 1.0
CA C:LYS164 4.3 10.8 1.0
C C:HIS162 4.3 10.5 1.0
O C:HOH510 4.4 23.5 1.0
CG C:ASP163 4.5 17.8 1.0
CG C:GLU161 4.5 12.6 1.0
CE C:LYS164 4.6 27.0 1.0
CA C:HIS162 4.6 9.3 1.0
O C:HOH521 4.8 22.6 1.0
N C:GLU161 4.9 9.7 1.0
OD2 C:ASP163 4.9 17.2 1.0

Chlorine binding site 5 out of 6 in 3vty

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Chlorine binding site 5 out of 6 in the Crystal Structure of Mama


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Mama within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl301

b:11.4
occ:1.00
 O D:HOH462 3.0 26.8 1.0
O D:HOH477 3.1 27.8 1.0
O D:HOH501 3.1 29.2 1.0
N D:LYS164 3.3 9.6 1.0
C D:GLU161 3.4 11.3 1.0
N D:ASP163 3.4 12.3 1.0
CA D:GLU161 3.4 10.6 1.0
CB D:ASP163 3.6 12.0 1.0
CB D:GLU161 3.6 10.3 1.0
O D:GLU161 3.7 10.9 1.0
N D:HIS162 3.7 11.7 1.0
CG D:LYS164 3.8 13.8 1.0
CA D:ASP163 3.8 11.7 1.0
CB D:LYS164 4.1 10.9 1.0
C D:ASP163 4.1 11.3 1.0
O D:HOH435 4.1 23.3 1.0
CA D:LYS164 4.3 9.2 1.0
C D:HIS162 4.4 11.5 1.0
CD D:LYS164 4.4 18.4 1.0
CG D:ASP163 4.4 17.9 1.0
CG D:GLU161 4.5 13.1 1.0
OD2 D:ASP163 4.6 21.4 1.0
CA D:HIS162 4.6 11.0 1.0
O D:HOH457 4.7 27.6 1.0
CE D:LYS164 4.7 24.4 1.0
O D:HOH463 4.8 24.5 1.0
OE1 D:GLU161 4.9 18.8 1.0
N D:GLU161 4.9 11.6 1.0

Chlorine binding site 6 out of 6 in 3vty

Go back to Chlorine Binding Sites List in 3vty
Chlorine binding site 6 out of 6 in the Crystal Structure of Mama


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Mama within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl302

b:24.1
occ:1.00
 NE D:ARG181 3.1 16.1 1.0
O C:HOH529 3.1 29.7 1.0
N D:ILE180 3.3 17.2 1.0
N D:ARG181 3.3 15.4 1.0
O D:HOH541 3.7 42.0 1.0
CG D:ARG181 3.7 13.8 1.0
CB D:ARG181 3.7 13.8 1.0
CB D:ILE180 3.8 18.6 1.0
CD D:ARG181 3.9 16.6 1.0
NH2 D:ARG181 3.9 24.2 1.0
CA D:ILE180 3.9 17.8 1.0
CD1 D:PHE179 4.0 13.9 1.0
CZ D:ARG181 4.0 18.5 1.0
C D:PHE179 4.0 15.9 1.0
C D:ILE180 4.2 16.4 1.0
CA D:ARG181 4.2 13.2 1.0
CE1 D:PHE179 4.3 15.9 1.0
CA D:PHE179 4.3 16.9 1.0
CG D:PHE179 4.6 15.4 1.0
O D:GLY178 4.6 20.3 1.0
O C:HOH560 4.7 37.3 1.0
CG1 D:ILE180 4.7 23.8 1.0
O D:PHE179 4.7 14.6 1.0
CG2 D:ILE180 4.9 21.0 1.0
O D:HOH576 4.9 55.4 1.0

Reference:

N.Zeytuni, D.Baran, G.Davidov, R.Zarivach. Inter-Phylum Structural Conservation of the Magnetosome-Associated Tpr-Containing Protein, Mama J.Struct.Biol. V. 180 479 2012.
ISSN: ISSN 1047-8477
PubMed: 22917855
DOI: 10.1016/J.JSB.2012.08.001
Page generated: Sat Dec 12 10:18:21 2020

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