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Chlorine in PDB 9rm2: Bkpyv VP1 in Complex with 319C07-Fab

Protein crystallography data

The structure of Bkpyv VP1 in Complex with 319C07-Fab, PDB code: 9rm2 was solved by S.Schmitt, M.Hillenbrand, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 91.87 / 1.96
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 109.349, 172.078, 113.144, 90, 97.64, 90
R / Rfree (%) 18.7 / 21.8

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Bkpyv VP1 in Complex with 319C07-Fab (pdb code 9rm2). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Bkpyv VP1 in Complex with 319C07-Fab, PDB code: 9rm2:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 9rm2

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Chlorine binding site 1 out of 9 in the Bkpyv VP1 in Complex with 319C07-Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Bkpyv VP1 in Complex with 319C07-Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl301

b:53.2
occ:1.00
 O B:HOH486 2.9 48.9 1.0
NH1 H:ARG54 3.3 40.7 1.0
ND2 H:ASN52 3.3 37.6 1.0
CD H:ARG54 3.6 37.8 1.0
CD2 H:TYR56 3.7 37.2 1.0
CE2 H:TYR56 3.8 38.8 1.0
O H:HOH427 4.1 50.5 1.0
C2 H:PGE303 4.1 68.6 1.0
CG H:ARG54 4.1 37.4 1.0
O C:HOH528 4.1 44.0 1.0
CZ H:ARG54 4.2 39.4 1.0
CB H:ARG54 4.2 36.6 1.0
NE H:ARG54 4.3 40.4 1.0
CG H:ASN52 4.4 37.0 1.0
O2 H:PGE303 4.5 66.4 1.0
C3 H:PGE303 4.5 66.9 1.0
OD1 H:ASN52 4.6 35.0 1.0
O B:GLY58 4.7 35.0 1.0
CG H:TYR56 4.8 38.4 1.0
CZ H:TYR56 4.9 39.7 1.0

Chlorine binding site 2 out of 9 in 9rm2

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Chlorine binding site 2 out of 9 in the Bkpyv VP1 in Complex with 319C07-Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Bkpyv VP1 in Complex with 319C07-Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Cl301

b:37.1
occ:1.00
 N P:LYS156 3.2 31.9 1.0
O P:HOH572 3.3 54.5 1.0
ND1 P:HIS169 3.6 27.9 1.0
O P:HOH413 3.6 51.9 1.0
CA P:HIS169 3.7 30.1 1.0
CA P:PRO155 3.8 31.5 1.0
CB P:LYS156 3.9 40.2 1.0
O P:ASP168 4.0 31.7 1.0
C P:PRO155 4.0 31.7 1.0
O P:HOH481 4.1 57.8 1.0
CA P:LYS156 4.1 35.8 1.0
CH2 P:TRP184 4.1 28.9 1.0
CB P:HIS169 4.2 29.4 1.0
CG P:LYS156 4.2 44.8 1.0
O P:LYS156 4.3 35.3 1.0
N P:LYS170 4.3 30.8 1.0
CG P:HIS169 4.3 29.1 1.0
C P:HIS169 4.3 30.8 1.0
O P:LYS170 4.5 32.6 1.0
N P:HIS169 4.5 31.2 1.0
C P:ASP168 4.6 33.5 1.0
O P:THR154 4.6 28.9 1.0
CD P:LYS156 4.6 49.7 1.0
CE1 P:HIS169 4.6 28.7 1.0
CB P:PRO155 4.7 31.3 1.0
C P:LYS156 4.7 34.6 1.0
N P:PRO155 4.8 30.7 1.0
CZ2 P:TRP184 4.9 28.7 1.0
CZ3 P:TRP184 5.0 28.0 1.0

Chlorine binding site 3 out of 9 in 9rm2

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Chlorine binding site 3 out of 9 in the Bkpyv VP1 in Complex with 319C07-Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Bkpyv VP1 in Complex with 319C07-Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:75.6
occ:1.00
 O E:HOH496 3.7 71.1 1.0
CE1 A:TYR56 4.1 46.3 1.0
O A:ARG54 4.2 44.1 1.0
NH2 E:ARG46 4.2 35.5 1.0
CZ E:ARG46 4.3 35.3 1.0
CD1 A:TYR56 4.4 45.2 1.0
O A:GLY55 4.4 40.6 1.0
CZ A:TYR56 4.5 47.5 1.0
NH1 E:ARG46 4.6 36.6 1.0
C A:GLY55 4.6 42.4 1.0
CL E:CL301 4.6 55.2 1.0
O E:HOH492 4.6 51.0 1.0
NE E:ARG46 4.8 34.1 1.0
OH A:TYR56 4.9 50.7 1.0
N A:TYR56 4.9 41.2 1.0

Chlorine binding site 4 out of 9 in 9rm2

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Chlorine binding site 4 out of 9 in the Bkpyv VP1 in Complex with 319C07-Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Bkpyv VP1 in Complex with 319C07-Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl301

b:35.2
occ:1.00
 N C:LYS156 3.2 34.2 1.0
O C:HOH497 3.2 57.8 1.0
ND1 C:HIS169 3.4 31.8 1.0
CA C:HIS169 3.5 33.0 1.0
O C:HOH550 3.6 52.0 1.0
CA C:PRO155 3.7 32.4 1.0
O C:ASP168 3.9 34.6 1.0
C C:PRO155 4.0 33.0 1.0
CB C:HIS169 4.0 32.2 1.0
CB C:LYS156 4.1 37.0 1.0
CG C:HIS169 4.1 29.9 1.0
CA C:LYS156 4.2 36.4 1.0
O C:HOH573 4.2 53.5 1.0
CG C:LYS156 4.2 40.2 1.0
O C:LYS156 4.2 35.9 1.0
N C:LYS170 4.2 34.5 1.0
CH2 C:TRP184 4.2 28.4 1.0
C C:HIS169 4.3 33.4 1.0
O C:HOH536 4.4 55.8 1.0
CE1 C:HIS169 4.4 31.7 1.0
N C:HIS169 4.4 33.9 1.0
C C:ASP168 4.5 35.5 1.0
O C:LYS170 4.5 36.3 1.0
CB C:PRO155 4.6 31.9 1.0
O C:THR154 4.7 33.9 1.0
C C:LYS156 4.7 37.2 1.0
N C:PRO155 4.7 32.4 1.0

Chlorine binding site 5 out of 9 in 9rm2

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Chlorine binding site 5 out of 9 in the Bkpyv VP1 in Complex with 319C07-Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Bkpyv VP1 in Complex with 319C07-Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl301

b:55.2
occ:1.00
 O E:HOH424 3.0 60.7 1.0
NH1 E:ARG46 3.1 36.6 1.0
O E:HOH418 3.1 39.2 1.0
NH2 E:ARG46 3.2 35.5 1.0
NH2 E:ARG62 3.4 36.5 1.0
CZ E:ARG46 3.6 35.3 1.0
CG E:PRO60 3.7 37.4 1.0
CE1 A:TYR56 3.8 46.3 1.0
CD E:PRO60 4.0 36.0 1.0
CE2 E:PHE63 4.2 39.4 1.0
CZ E:ARG62 4.4 37.4 1.0
OH A:TYR56 4.5 50.7 1.0
O E:HOH492 4.5 51.0 1.0
OD1 E:ASP83 4.6 43.7 1.0
CZ A:TYR56 4.6 47.5 1.0
CG E:GLU82 4.6 49.3 1.0
CL A:CL301 4.6 75.6 1.0
CD1 A:TYR56 4.6 45.2 1.0
CZ E:PHE63 4.7 37.0 1.0
NH1 E:ARG62 4.7 39.4 1.0
OE2 E:GLU82 4.9 52.8 1.0
NE E:ARG46 4.9 34.1 1.0
O E:HOH491 5.0 52.6 1.0

Chlorine binding site 6 out of 9 in 9rm2

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Chlorine binding site 6 out of 9 in the Bkpyv VP1 in Complex with 319C07-Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Bkpyv VP1 in Complex with 319C07-Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl301

b:36.1
occ:1.00
 N F:LYS156 3.2 35.0 1.0
ND1 F:HIS169 3.5 28.1 1.0
CA F:HIS169 3.7 31.2 1.0
CA F:PRO155 3.8 31.4 1.0
C F:PRO155 4.0 33.0 1.0
O F:ASP168 4.0 32.1 1.0
CB F:LYS156 4.1 38.4 1.0
CH2 F:TRP184 4.2 27.2 1.0
CG F:LYS156 4.2 41.6 1.0
CB F:HIS169 4.2 30.6 1.0
CA F:LYS156 4.2 36.1 1.0
CG F:HIS169 4.3 29.0 1.0
O F:LYS156 4.3 33.4 1.0
C F:HIS169 4.4 31.1 1.0
N F:LYS170 4.4 30.8 1.0
CE1 F:HIS169 4.4 29.3 1.0
N F:HIS169 4.5 30.9 1.0
O F:LYS170 4.6 34.2 1.0
C F:ASP168 4.6 32.7 1.0
CB F:PRO155 4.6 31.3 1.0
O F:THR154 4.7 30.3 1.0
N F:PRO155 4.8 30.4 1.0
C F:LYS156 4.8 36.2 1.0
CD F:LYS156 4.9 45.3 1.0
CZ2 F:TRP184 4.9 27.1 1.0
CZ3 F:TRP184 5.0 27.1 1.0

Chlorine binding site 7 out of 9 in 9rm2

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Chlorine binding site 7 out of 9 in the Bkpyv VP1 in Complex with 319C07-Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Bkpyv VP1 in Complex with 319C07-Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl301

b:35.0
occ:1.00
 N K:LYS156 3.2 33.9 1.0
ND1 K:HIS169 3.5 31.5 1.0
CA K:HIS169 3.6 31.3 1.0
CA K:PRO155 3.7 30.3 1.0
CG K:LYS156 3.8 45.8 1.0
O K:HOH510 3.8 50.4 1.0
O K:ASP168 3.9 34.3 1.0
C K:PRO155 4.0 32.3 1.0
CB K:HIS169 4.1 31.6 1.0
CH2 K:TRP184 4.1 25.9 1.0
CB K:LYS156 4.1 40.4 1.0
CA K:LYS156 4.2 37.3 1.0
CG K:HIS169 4.2 31.3 1.0
N K:LYS170 4.3 28.9 1.0
C K:HIS169 4.3 29.9 1.0
O K:LYS156 4.3 31.1 1.0
N K:HIS169 4.4 33.2 1.0
O K:LYS170 4.4 33.5 1.0
CE1 K:HIS169 4.5 32.1 1.0
C K:ASP168 4.5 35.3 1.0
CB K:PRO155 4.6 29.6 1.0
O K:HOH611 4.6 61.5 1.0
O K:THR154 4.7 28.3 1.0
N K:PRO155 4.7 29.5 1.0
C K:LYS156 4.8 34.5 1.0
CD K:LYS156 4.8 48.8 1.0
CZ2 K:TRP184 4.9 25.4 1.0
CZ3 K:TRP184 4.9 26.1 1.0

Chlorine binding site 8 out of 9 in 9rm2

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Chlorine binding site 8 out of 9 in the Bkpyv VP1 in Complex with 319C07-Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Bkpyv VP1 in Complex with 319C07-Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cl301

b:57.1
occ:1.00
 NH1 M:ARG54 3.1 43.3 1.0
ND2 M:ASN52 3.3 36.3 1.0
CE2 M:TYR56 3.5 40.6 1.0
CD2 M:TYR56 3.6 38.9 1.0
CD M:ARG54 3.7 39.1 1.0
O M:HOH470 3.9 39.4 1.0
CG M:ARG54 4.0 38.6 1.0
O P:HOH516 4.0 53.9 1.0
CZ M:ARG54 4.1 42.6 1.0
O M:HOH477 4.2 55.0 1.0
CB M:ARG54 4.3 37.6 1.0
NE M:ARG54 4.3 40.8 1.0
CG M:ASN52 4.4 35.4 1.0
O L:GLY58 4.5 39.2 1.0
CZ M:TYR56 4.6 41.8 1.0
CG M:TYR56 4.6 37.4 1.0
OD1 M:ASN52 4.7 32.0 1.0
O M:HOH523 4.7 59.1 1.0
O P:HOH511 4.8 31.6 1.0
CA L:GLY58 5.0 36.9 1.0

Chlorine binding site 9 out of 9 in 9rm2

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Chlorine binding site 9 out of 9 in the Bkpyv VP1 in Complex with 319C07-Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Bkpyv VP1 in Complex with 319C07-Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cl301

b:35.4
occ:1.00
 N O:LYS156 3.2 33.2 1.0
O O:HOH572 3.4 48.9 1.0
ND1 O:HIS169 3.4 26.9 1.0
CA O:HIS169 3.6 28.5 1.0
CA O:PRO155 3.7 31.1 1.0
C O:PRO155 4.0 31.4 1.0
CB O:LYS156 4.0 36.4 1.0
O O:ASP168 4.0 32.5 1.0
CB O:HIS169 4.1 26.9 1.0
CA O:LYS156 4.1 33.8 1.0
CG O:HIS169 4.2 25.9 1.0
CG O:LYS156 4.2 40.3 1.0
CH2 O:TRP184 4.2 26.1 1.0
O O:LYS156 4.3 31.2 1.0
C O:HIS169 4.4 29.1 1.0
N O:LYS170 4.4 31.4 1.0
CE1 O:HIS169 4.4 27.9 1.0
N O:HIS169 4.5 29.8 1.0
C O:ASP168 4.6 33.0 1.0
O O:LYS170 4.6 33.5 1.0
CB O:PRO155 4.6 30.2 1.0
O O:THR154 4.6 30.6 1.0
N O:PRO155 4.8 29.6 1.0
C O:LYS156 4.8 32.7 1.0

Reference:

M.Weber, M.Hillenbrand. A Highly Potent Human Antibody Neutralizing All Serotypes of Bk Polyomavirus To Be Published.
Page generated: Mon Aug 4 21:15:25 2025

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