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Chlorine in PDB 4qh0: Crystal Structure of Nuca From Streptococcus Agalactiae with Magnesium Ion Bound

Protein crystallography data

The structure of Crystal Structure of Nuca From Streptococcus Agalactiae with Magnesium Ion Bound, PDB code: 4qh0 was solved by A.F.Moon, P.Gaudu, L.C.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.85 / 2.00
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 123.721, 123.721, 157.403, 90.00, 90.00, 120.00
R / Rfree (%) 15.5 / 19

Other elements in 4qh0:

The structure of Crystal Structure of Nuca From Streptococcus Agalactiae with Magnesium Ion Bound also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Nuca From Streptococcus Agalactiae with Magnesium Ion Bound (pdb code 4qh0). 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 Nuca From Streptococcus Agalactiae with Magnesium Ion Bound, PDB code: 4qh0:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4qh0

Go back to Chlorine Binding Sites List in 4qh0
Chlorine binding site 1 out of 6 in the Crystal Structure of Nuca From Streptococcus Agalactiae with Magnesium Ion Bound


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 Nuca From Streptococcus Agalactiae with Magnesium Ion Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl307

b:41.4
occ:1.00
 O A:HOH440 3.0 38.5 1.0
O A:HOH573 3.2 39.7 1.0
N A:ALA247 3.4 30.9 1.0
CG A:HIS177 3.5 27.5 1.0
O A:HOH444 3.5 42.9 1.0
CB A:HIS177 3.6 26.6 1.0
ND1 A:HIS177 3.6 26.7 1.0
CG A:GLN246 3.6 28.6 1.0
CE2 A:TYR140 3.7 31.9 1.0
CB A:ALA247 4.0 38.9 1.0
CA A:GLN246 4.1 30.4 1.0
CD2 A:HIS177 4.1 23.3 1.0
CE1 A:HIS177 4.2 27.2 1.0
C A:GLN246 4.3 36.1 1.0
CA A:ALA247 4.3 40.2 1.0
OH A:TYR140 4.3 34.8 1.0
CB A:GLN246 4.4 33.4 1.0
O A:HOH534 4.5 43.5 1.0
CZ A:TYR140 4.5 33.4 1.0
CD2 A:TYR140 4.5 31.3 1.0
NE2 A:HIS177 4.5 24.7 1.0
CD A:GLN246 4.6 28.6 1.0
CA A:HIS177 4.9 23.4 1.0

Chlorine binding site 2 out of 6 in 4qh0

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Chlorine binding site 2 out of 6 in the Crystal Structure of Nuca From Streptococcus Agalactiae with Magnesium Ion Bound


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 Nuca From Streptococcus Agalactiae with Magnesium Ion Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl308

b:40.1
occ:1.00
 NH1 A:ARG108 3.1 24.5 1.0
N D:LYS159 3.2 21.5 1.0
O D:HOH515 3.2 36.3 1.0
O D:HOH546 3.6 40.1 1.0
O D:HOH500 3.6 31.3 1.0
NH2 A:ARG108 3.8 25.4 1.0
O D:ASN157 3.8 28.0 1.0
CD1 D:PHE158 3.8 20.1 1.0
CB D:LYS159 3.8 28.3 1.0
CZ A:ARG108 3.9 23.8 1.0
CA D:PHE158 3.9 24.1 1.0
CD D:LYS159 4.0 30.5 1.0
C D:PHE158 4.0 24.6 1.0
CA D:LYS159 4.1 21.5 1.0
CG D:LYS159 4.2 27.5 1.0
O D:HOH510 4.3 38.7 1.0
CE1 D:PHE158 4.4 25.3 1.0
CG2 D:ILE110 4.5 26.0 1.0
CG D:PHE158 4.6 20.9 1.0
C D:ASN157 4.7 25.0 1.0
O D:LYS159 4.7 24.1 1.0
O D:HOH444 4.7 28.8 1.0
N D:PHE158 4.8 25.1 1.0
CB D:PHE158 4.8 19.8 1.0
O D:HOH563 4.8 46.4 1.0
C D:LYS159 4.9 25.4 1.0
CE D:LYS159 5.0 37.0 1.0

Chlorine binding site 3 out of 6 in 4qh0

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Chlorine binding site 3 out of 6 in the Crystal Structure of Nuca From Streptococcus Agalactiae with Magnesium Ion Bound


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 Nuca From Streptococcus Agalactiae with Magnesium Ion Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl308

b:55.3
occ:1.00
 O C:HOH478 2.8 40.0 1.0
N C:ASN80 3.1 43.1 1.0
O C:HOH559 3.5 47.5 1.0
O C:HOH541 3.5 51.5 1.0
CB C:ASN80 3.5 51.4 1.0
O B:HOH479 3.8 33.8 1.0
CA C:ASN80 3.8 45.6 1.0
NE C:ARG207 3.8 27.4 1.0
NH2 C:ARG207 3.8 26.6 1.0
C C:LEU79 4.1 38.5 1.0
CA C:LEU79 4.1 29.3 1.0
O C:ASN80 4.1 47.0 1.0
CZ C:ARG207 4.2 25.2 1.0
CD2 C:LEU79 4.3 23.8 1.0
C C:ASN80 4.4 39.9 1.0
O B:HOH450 4.5 41.4 1.0
CB C:LEU79 4.8 28.7 1.0
CD C:ARG207 4.8 24.7 1.0
CG C:ASN80 4.8 56.1 1.0
O C:ASN78 4.9 37.4 1.0
CG C:ARG207 4.9 27.2 1.0

Chlorine binding site 4 out of 6 in 4qh0

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Chlorine binding site 4 out of 6 in the Crystal Structure of Nuca From Streptococcus Agalactiae with Magnesium Ion Bound


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 Nuca From Streptococcus Agalactiae with Magnesium Ion Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl309

b:43.5
occ:1.00
 O C:HOH494 3.1 48.1 1.0
N C:ARG205 3.3 31.9 1.0
N C:ASP233 3.3 39.5 1.0
CB C:LYS204 3.3 37.1 1.0
CA C:LYS204 3.4 34.3 1.0
CG C:ASP233 3.5 37.5 1.0
N C:GLN232 3.5 34.4 1.0
CB C:GLN232 3.6 44.8 1.0
OD1 C:ASP233 3.6 36.8 1.0
CG C:LYS204 3.7 37.5 1.0
OD2 C:ASP233 3.7 41.3 1.0
C C:LYS204 3.8 28.8 1.0
CA C:GLN232 3.9 35.8 1.0
CB C:ASP233 3.9 32.6 1.0
O C:ARG205 4.0 33.8 1.0
C C:GLN232 4.0 39.5 1.0
CB C:SER231 4.1 29.1 1.0
CA C:ASP233 4.2 37.6 1.0
C C:SER231 4.4 31.8 1.0
CA C:ARG205 4.4 32.1 1.0
C C:ARG205 4.6 28.0 1.0
CD C:LYS204 4.6 32.9 1.0
OG C:SER231 4.6 31.2 1.0
CA C:SER231 4.7 30.0 1.0
N C:LYS204 4.7 36.1 1.0
CB C:ARG205 4.7 33.1 1.0
CG C:GLN232 4.8 50.4 1.0
O C:ASN203 4.8 40.2 1.0

Chlorine binding site 5 out of 6 in 4qh0

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Chlorine binding site 5 out of 6 in the Crystal Structure of Nuca From Streptococcus Agalactiae with Magnesium Ion Bound


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 Nuca From Streptococcus Agalactiae with Magnesium Ion Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl310

b:38.9
occ:1.00
 N D:ASP233 3.2 37.1 1.0
N D:GLN232 3.4 33.2 1.0
CB D:LYS204 3.4 30.5 1.0
N D:ARG205 3.5 28.6 1.0
CA D:LYS204 3.5 25.9 1.0
CB D:GLN232 3.5 40.6 1.0
CG D:ASP233 3.5 29.4 1.0
OD1 D:ASP233 3.7 34.0 1.0
OD2 D:ASP233 3.8 32.8 1.0
CA D:GLN232 3.8 38.0 1.0
CB D:ASP233 3.9 33.6 1.0
CG D:LYS204 3.9 31.4 1.0
CB D:SER231 3.9 26.7 1.0
C D:LYS204 4.0 25.4 1.0
C D:GLN232 4.0 40.0 1.0
O D:ARG205 4.0 33.0 1.0
CG D:GLN232 4.1 43.8 1.0
CA D:ASP233 4.2 34.6 1.0
C D:SER231 4.2 30.2 1.0
CD D:LYS204 4.4 30.6 1.0
OG D:SER231 4.5 30.3 1.0
CA D:SER231 4.5 32.6 1.0
CA D:ARG205 4.5 29.3 1.0
C D:ARG205 4.6 28.4 1.0
NE2 D:GLN232 4.8 39.8 1.0
N D:LYS204 4.8 26.5 1.0
CD D:GLN232 4.9 46.9 1.0
O D:ASN203 5.0 36.0 1.0
CB D:ARG205 5.0 34.8 1.0

Chlorine binding site 6 out of 6 in 4qh0

Go back to Chlorine Binding Sites List in 4qh0
Chlorine binding site 6 out of 6 in the Crystal Structure of Nuca From Streptococcus Agalactiae with Magnesium Ion Bound


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 Nuca From Streptococcus Agalactiae with Magnesium Ion Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl311

b:37.0
occ:1.00
 N D:ALA247 3.3 29.0 1.0
O D:HOH481 3.4 31.2 1.0
CG D:HIS177 3.5 26.2 1.0
ND1 D:HIS177 3.5 26.9 1.0
CB D:HIS177 3.6 25.8 1.0
CE2 D:TYR140 3.7 25.9 1.0
CB D:ALA247 3.8 35.2 1.0
CG D:GLN246 3.9 24.9 1.0
CA D:GLN246 4.1 28.9 1.0
CD2 D:HIS177 4.1 22.6 1.0
CE1 D:HIS177 4.1 26.7 1.0
CA D:ALA247 4.2 30.9 1.0
C D:GLN246 4.2 32.6 1.0
NE2 D:HIS177 4.5 26.2 1.0
OH D:TYR140 4.5 32.0 1.0
CD2 D:TYR140 4.6 27.2 1.0
CZ D:TYR140 4.6 26.5 1.0
CB D:GLN246 4.6 26.2 1.0
O3 D:SO4305 4.8 52.2 0.9
CD D:GLN246 4.9 23.3 1.0
ND2 D:ASN186 4.9 28.2 1.0
CA D:HIS177 5.0 25.9 1.0

Reference:

A.F.Moon, P.Gaudu, L.C.Pedersen. Structural Characterization of the Virulence Factor Nuclease A From Streptococcus Agalactiae. Acta Crystallogr.,Sect.D V. 70 2937 2014.
ISSN: ISSN 0907-4449
PubMed: 25372684
DOI: 10.1107/S1399004714019725
Page generated: Fri Jul 26 00:31:09 2024

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