Chlorine in PDB 5bnq: Crystal Structure of Hrankl-Mrank Complex

Protein crystallography data

The structure of Crystal Structure of Hrankl-Mrank Complex, PDB code: 5bnq was solved by J.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.37 / 2.80
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 122.188, 122.188, 94.473, 90.00, 90.00, 120.00
R / Rfree (%) 17.1 / 20.3

Other elements in 5bnq:

The structure of Crystal Structure of Hrankl-Mrank Complex also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Hrankl-Mrank Complex (pdb code 5bnq). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of Hrankl-Mrank Complex, PDB code: 5bnq:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 5bnq

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Chlorine binding site 1 out of 8 in the Crystal Structure of Hrankl-Mrank Complex


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 Hrankl-Mrank Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:36.7
occ:0.33
 NZ A:LYS262 3.1 31.8 1.0
CE1 A:TYR273 3.8 31.0 1.0
CE A:LYS262 3.9 30.6 1.0
O A:HOH525 4.1 13.4 0.3
CD1 A:TYR273 4.2 33.1 1.0
O A:HOH519 4.3 2.0 0.3
OG A:SER260 4.5 33.0 1.0
CB A:SER260 4.8 30.5 1.0
CZ A:TYR273 4.8 33.0 1.0

Chlorine binding site 2 out of 8 in 5bnq

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Chlorine binding site 2 out of 8 in the Crystal Structure of Hrankl-Mrank Complex


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 Hrankl-Mrank Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:57.4
occ:1.00
 ND1 A:HIS271 3.3 45.8 1.0
CD1 A:TRP264 3.6 35.6 1.0
NE1 A:TRP264 3.7 33.0 1.0
O A:HOH516 3.8 22.2 1.0
CE1 A:HIS271 4.0 44.4 1.0
O A:HOH529 4.0 45.2 1.0
O A:TYR263 4.2 44.4 1.0
CG A:HIS271 4.4 42.0 1.0
CG A:TRP264 4.6 36.4 1.0
CB A:HIS271 4.7 37.0 1.0
CE2 A:TRP264 4.8 33.6 1.0
O A:HOH518 5.0 48.5 1.0

Chlorine binding site 3 out of 8 in 5bnq

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Chlorine binding site 3 out of 8 in the Crystal Structure of Hrankl-Mrank Complex


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 Hrankl-Mrank Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:43.7
occ:1.00
 N A:LYS282 3.2 40.3 1.0
NZ R:LYS86 3.3 70.0 1.0
CD2 A:PHE281 3.8 35.4 1.0
CB A:LYS282 3.8 43.4 1.0
CA A:PHE281 3.9 36.0 1.0
CB A:PHE281 4.0 34.0 1.0
C A:PHE281 4.0 39.3 1.0
CA A:LYS282 4.1 42.1 1.0
CE R:LYS86 4.1 67.8 1.0
O A:LYS282 4.1 46.2 1.0
CG A:PHE281 4.4 34.8 1.0
C A:LYS282 4.6 41.4 1.0
O R:HOH413 4.8 43.0 1.0
CE2 A:PHE281 4.8 35.9 1.0
O A:PHE280 4.9 41.1 1.0

Chlorine binding site 4 out of 8 in 5bnq

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Chlorine binding site 4 out of 8 in the Crystal Structure of Hrankl-Mrank Complex


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 Hrankl-Mrank Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:53.5
occ:1.00
 N A:ASP190 3.1 48.8 1.0
N A:HIS189 3.2 39.5 1.0
NE A:ARG191 3.2 42.7 1.0
CA A:TYR188 3.7 38.9 1.0
CB A:TYR188 3.8 39.6 1.0
ND1 A:HIS189 3.8 55.2 1.0
C A:ASP190 3.8 50.4 1.0
CA A:ASP190 3.9 50.0 1.0
NH2 A:ARG191 3.9 44.3 1.0
C A:TYR188 3.9 40.7 1.0
CG A:ARG191 4.0 41.6 1.0
CZ A:ARG191 4.0 44.6 1.0
C A:HIS189 4.1 47.8 1.0
CE1 A:HIS189 4.1 57.9 1.0
CA A:HIS189 4.1 43.5 1.0
CD A:ARG191 4.1 40.2 1.0
N A:ARG191 4.1 44.4 1.0
O A:ASP190 4.2 60.6 1.0
CD2 A:TYR188 4.2 39.1 1.0
CG A:HIS189 4.2 51.2 1.0
CB A:ASP190 4.3 55.0 1.0
CG A:TYR188 4.4 41.3 1.0
CB A:ARG191 4.5 41.4 1.0
NE2 A:HIS189 4.6 56.4 1.0
CD2 A:HIS189 4.7 51.8 1.0
CB A:HIS189 4.7 44.9 1.0
CA A:ARG191 4.9 41.7 1.0

Chlorine binding site 5 out of 8 in 5bnq

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Chlorine binding site 5 out of 8 in the Crystal Structure of Hrankl-Mrank Complex


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 Hrankl-Mrank Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:78.6
occ:1.00
 NH2 R:ARG130 4.3 67.6 1.0
CG A:TYR235 4.5 55.6 1.0
CD1 A:TYR235 4.6 57.8 1.0
CD2 A:TYR235 4.7 55.6 1.0
CB A:TYR235 4.8 47.9 1.0
CE1 A:TYR235 4.9 61.0 1.0

Chlorine binding site 6 out of 8 in 5bnq

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Chlorine binding site 6 out of 8 in the Crystal Structure of Hrankl-Mrank Complex


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 Hrankl-Mrank Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Cl305

b:49.1
occ:1.00
 N R:LYS91 3.2 36.5 1.0
N R:ARG111 3.2 53.0 1.0
NZ R:LYS91 3.3 41.2 1.0
CA R:HIS90 3.6 42.4 1.0
CB R:PRO110 3.7 48.6 1.0
O R:ARG111 3.7 48.7 1.0
CG R:LYS91 3.7 34.8 1.0
CA R:PRO110 3.8 51.6 1.0
CE2 R:TYR77 3.9 47.6 1.0
CD2 R:HIS90 3.9 50.6 1.0
C R:HIS90 3.9 41.1 1.0
CE R:LYS91 4.0 38.6 1.0
C R:PRO110 4.0 55.6 1.0
CB R:ARG111 4.0 46.5 1.0
CA R:ARG111 4.0 49.4 1.0
CB R:LYS91 4.1 34.8 1.0
CB R:HIS90 4.1 44.7 1.0
OH R:TYR77 4.1 53.7 1.0
CA R:LYS91 4.2 35.0 1.0
CZ R:TYR77 4.3 51.3 1.0
C R:ARG111 4.3 50.0 1.0
CG R:HIS90 4.4 48.8 1.0
CD R:LYS91 4.4 36.5 1.0
O R:LEU89 4.6 47.0 1.0
CD2 R:TYR77 4.7 49.9 1.0
N R:HIS90 4.7 42.0 1.0

Chlorine binding site 7 out of 8 in 5bnq

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Chlorine binding site 7 out of 8 in the Crystal Structure of Hrankl-Mrank Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Hrankl-Mrank Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Cl306

b:73.9
occ:1.00
 NE2 R:HIS120 3.3 52.2 1.0
ND2 R:ASN122 3.7 56.8 1.0
CE1 R:HIS120 3.9 52.7 1.0
CB R:ARG129 4.3 48.8 1.0
NH1 R:ARG129 4.4 62.5 1.0
CD2 R:HIS120 4.4 49.8 1.0
CG R:ARG129 4.5 52.8 1.0
CZ R:ARG129 4.5 65.4 1.0
NH2 R:ARG129 4.8 62.0 1.0
OD2 R:ASP149 4.8 52.3 1.0
CG R:ASN122 4.8 53.5 1.0
NE R:ARG129 4.9 63.0 1.0

Chlorine binding site 8 out of 8 in 5bnq

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Chlorine binding site 8 out of 8 in the Crystal Structure of Hrankl-Mrank Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Hrankl-Mrank Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Cl307

b:66.4
occ:1.00
 O R:VAL92 4.3 37.8 1.0
CD1 R:LEU99 4.5 39.8 1.0
NZ R:LYS97 4.8 38.4 1.0
CH2 R:TRP121 4.8 39.2 1.0
CD R:LYS97 5.0 37.4 1.0

Reference:

C.Liu, Y.Zhao, W.He, W.Wang, Y.Chen, S.Zhang, Y.Ma, J.Gohda, T.Ishida, T.S.Walter, R.J.Owens, D.I.Stuart, J.Ren, B.Gao. A Rankl Mutant Used As An Inter-Species Vaccine For Efficient Immunotherapy of Osteoporosis. Sci Rep V. 5 14150 2015.
ISSN: ESSN 2045-2322
PubMed: 26412210
DOI: 10.1038/SREP14150
Page generated: Sat Dec 12 11:32:23 2020

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