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Chlorine in PDB 2ypy: Kshv Lana (ORF73) C-Terminal Domain, Decameric Ring: Monoclinic Crystal Form

Protein crystallography data

The structure of Kshv Lana (ORF73) C-Terminal Domain, Decameric Ring: Monoclinic Crystal Form, PDB code: 2ypy was solved by J.Hellert, J.Krausze, T.Luhrs, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.652 / 2.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.740, 175.920, 97.580, 90.00, 95.50, 90.00
R / Rfree (%) 22.07 / 25.22

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Chlorine atom in the Kshv Lana (ORF73) C-Terminal Domain, Decameric Ring: Monoclinic Crystal Form (pdb code 2ypy). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 24 binding sites of Chlorine where determined in the Kshv Lana (ORF73) C-Terminal Domain, Decameric Ring: Monoclinic Crystal Form, PDB code: 2ypy:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 24 in 2ypy

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Chlorine binding site 1 out of 24 in the Kshv Lana (ORF73) C-Terminal Domain, Decameric Ring: Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Kshv Lana (ORF73) C-Terminal Domain, Decameric Ring: Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2148

b:68.3
occ:1.00
 N B:ILE1136 3.3 48.4 1.0
NE2 B:GLN1116 3.5 57.2 1.0
CE A:LYS1141 3.5 78.3 1.0
CD A:LYS1140 3.5 83.4 1.0
CA B:SER1135 3.6 44.2 1.0
CB A:LYS1140 3.8 75.7 1.0
CG1 B:ILE1136 3.8 65.5 1.0
CG A:LYS1141 3.8 75.3 1.0
CD A:LYS1141 3.8 75.7 1.0
CG A:LYS1140 3.9 81.0 1.0
C B:SER1135 3.9 47.1 1.0
OE1 B:GLN1116 4.0 53.2 1.0
CB B:ILE1136 4.1 61.4 1.0
CD B:GLN1116 4.2 53.6 1.0
NZ A:LYS1141 4.2 79.0 1.0
CA B:ILE1136 4.3 52.0 1.0
OG B:SER1135 4.4 46.0 1.0
CB B:SER1135 4.4 44.7 1.0
CE A:LYS1140 4.4 86.5 1.0
O B:SER1134 4.4 58.8 1.0
CD1 B:ILE1136 4.5 71.5 1.0
N B:SER1135 4.6 42.9 1.0
N A:LYS1141 4.7 71.5 1.0
NZ A:LYS1140 4.7 87.2 1.0
CB A:LYS1141 4.7 73.4 1.0
C B:SER1134 4.8 51.2 1.0
CA A:LYS1140 4.9 73.1 1.0

Chlorine binding site 2 out of 24 in 2ypy

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Chlorine binding site 2 out of 24 in the Kshv Lana (ORF73) C-Terminal Domain, Decameric Ring: Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Kshv Lana (ORF73) C-Terminal Domain, Decameric Ring: Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2149

b:70.6
occ:1.00
 O A:HOH2004 3.2 42.1 1.0
N A:GLY1130 3.3 74.2 1.0
NH2 A:ARG1119 3.5 53.6 1.0
CA A:ALA1129 3.6 77.4 1.0
CA A:GLY1067 3.8 50.0 1.0
CB A:ALA1129 3.9 76.1 1.0
NZ A:LYS1070 3.9 51.7 1.0
C A:ALA1129 4.0 76.2 1.0
CE A:LYS1070 4.1 52.7 1.0
CA A:GLY1130 4.4 74.8 1.0
CZ A:ARG1119 4.5 54.4 1.0
NH1 A:ARG1119 4.6 53.6 1.0
O A:GLY1067 4.6 47.3 1.0
C A:GLY1067 4.6 47.1 1.0
N A:ALA1129 4.8 83.7 1.0
O A:LEU1128 4.9 86.6 1.0

Chlorine binding site 3 out of 24 in 2ypy

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Chlorine binding site 3 out of 24 in the Kshv Lana (ORF73) C-Terminal Domain, Decameric Ring: Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Kshv Lana (ORF73) C-Terminal Domain, Decameric Ring: Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2151

b:71.2
occ:1.00
 CE B:LYS1141 3.4 82.0 1.0
CD B:LYS1140 3.5 89.3 1.0
OE1 A:GLN1116 3.5 68.1 1.0
N A:ILE1136 3.5 66.5 1.0
CG B:LYS1141 3.6 76.8 1.0
CG1 A:ILE1136 3.6 73.1 1.0
CD B:LYS1141 3.7 77.9 1.0
CA A:SER1135 3.7 64.5 1.0
CB B:LYS1140 3.8 76.8 1.0
CG B:LYS1140 3.9 84.5 1.0
O A:SER1134 4.0 73.5 1.0
C A:SER1135 4.1 64.4 1.0
NE2 A:GLN1116 4.1 73.8 1.0
OG A:SER1135 4.2 64.5 1.0
NZ B:LYS1141 4.2 83.7 1.0
CD A:GLN1116 4.2 70.8 1.0
CE B:LYS1140 4.3 95.5 1.0
CD1 A:ILE1136 4.3 72.7 1.0
CB A:ILE1136 4.4 71.8 1.0
CB A:SER1135 4.4 64.0 1.0
CB B:LYS1141 4.5 73.2 1.0
CA A:ILE1136 4.5 66.4 1.0
NZ B:LYS1140 4.6 98.6 1.0
N A:SER1135 4.6 63.7 1.0
N B:LYS1141 4.6 70.3 1.0
C A:SER1134 4.7 67.0 1.0
C B:LYS1140 4.9 72.8 1.0
CA B:LYS1140 4.9 72.5 1.0

Chlorine binding site 4 out of 24 in 2ypy

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Chlorine binding site 4 out of 24 in the Kshv Lana (ORF73) C-Terminal Domain, Decameric Ring: Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Kshv Lana (ORF73) C-Terminal Domain, Decameric Ring: Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2152

b:52.7
occ:1.00
 NH2 B:ARG1119 3.0 46.3 1.0
O B:HOH2003 3.1 34.7 0.9
N B:GLY1130 3.3 51.9 1.0
CA B:ALA1129 3.7 57.9 1.0
CB B:ALA1129 3.8 55.3 1.0
CA B:GLY1067 3.8 38.3 1.0
C B:ALA1129 4.0 56.0 1.0
CZ B:ARG1119 4.0 46.0 1.0
NH1 B:ARG1119 4.1 44.9 1.0
CA B:GLY1130 4.3 52.2 1.0
O B:GLY1067 4.4 35.6 1.0
NZ B:LYS1070 4.4 52.6 1.0
C B:GLY1067 4.4 36.5 1.0
CE B:LYS1070 4.6 50.1 1.0
OD2 B:ASP1064 4.7 64.6 1.0
O B:GLY1130 4.8 53.8 1.0
N B:ALA1129 5.0 64.1 1.0

Chlorine binding site 5 out of 24 in 2ypy

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Chlorine binding site 5 out of 24 in the Kshv Lana (ORF73) C-Terminal Domain, Decameric Ring: Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Kshv Lana (ORF73) C-Terminal Domain, Decameric Ring: Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2153

b:79.9
occ:1.00
 NH1 B:ARG1039 2.8 75.2 1.0
NE2 B:HIS1035 3.9 43.5 1.0
CZ B:ARG1039 4.1 74.6 1.0
O B:GLN1076 4.1 45.5 1.0
O B:HOH2006 4.1 56.5 1.0
CE1 B:HIS1035 4.2 41.5 1.0
CB B:TYR1021 4.4 50.0 1.0
O B:TYR1021 4.5 61.7 1.0
NH2 B:ARG1039 4.7 77.2 1.0
CD1 B:PHE1077 4.7 45.9 1.0
C B:GLN1023 4.8 68.2 1.0
N B:ILE1024 4.8 64.8 1.0
CA B:GLN1023 4.9 75.2 1.0
CD2 B:TYR1021 4.9 43.6 1.0
C B:TYR1021 4.9 61.4 1.0

Chlorine binding site 6 out of 24 in 2ypy

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Chlorine binding site 6 out of 24 in the Kshv Lana (ORF73) C-Terminal Domain, Decameric Ring: Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Kshv Lana (ORF73) C-Terminal Domain, Decameric Ring: Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2154

b:90.2
occ:1.00
 NZ J:LYS1070 3.3 95.6 1.0
CE J:LYS1070 3.5 93.2 1.0
CA J:GLY1067 3.6 87.2 1.0
CA J:ALA1129 3.7 84.9 1.0
N J:GLY1130 3.8 80.8 1.0
CB J:ALA1129 3.8 82.3 1.0
NH2 J:ARG1119 4.0 72.4 1.0
C J:ALA1129 4.3 83.2 1.0
C J:GLY1067 4.5 82.6 1.0
O J:GLY1067 4.5 82.1 1.0
N J:GLY1067 4.7 90.8 1.0
NH1 J:ARG1119 4.8 70.9 1.0
CD J:LYS1070 4.8 92.7 1.0
N J:ALA1129 4.9 90.3 1.0
CZ J:ARG1119 4.9 69.9 1.0
CA J:GLY1130 4.9 80.8 1.0

Chlorine binding site 7 out of 24 in 2ypy

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Chlorine binding site 7 out of 24 in the Kshv Lana (ORF73) C-Terminal Domain, Decameric Ring: Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Kshv Lana (ORF73) C-Terminal Domain, Decameric Ring: Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl2149

b:48.7
occ:0.92
 NE2 C:GLN1116 3.1 53.4 1.0
N C:ILE1136 3.3 36.6 1.0
CG1 C:ILE1136 3.6 54.1 1.0
CG D:LYS1141 3.7 52.6 1.0
CA C:SER1135 3.7 37.4 1.0
OE1 C:GLN1116 3.7 53.1 1.0
CE D:LYS1141 3.8 60.2 1.0
CD D:LYS1140 3.8 56.2 1.0
CD C:GLN1116 3.9 51.0 1.0
C C:SER1135 3.9 34.4 1.0
CB D:LYS1140 4.0 47.3 1.0
CB C:ILE1136 4.1 50.5 1.0
CD D:LYS1141 4.1 58.1 1.0
CG D:LYS1140 4.1 52.8 1.0
CA C:ILE1136 4.3 42.9 1.0
OG C:SER1135 4.4 35.7 1.0
O C:SER1134 4.5 42.9 1.0
CB C:SER1135 4.6 36.7 1.0
CB D:LYS1141 4.6 49.5 1.0
N C:SER1135 4.6 39.5 1.0
CE D:LYS1140 4.7 60.1 1.0
CD1 C:ILE1136 4.7 55.0 1.0
N D:LYS1141 4.8 44.1 1.0
C C:SER1134 4.9 40.7 1.0
NZ D:LYS1141 4.9 65.1 1.0

Chlorine binding site 8 out of 24 in 2ypy

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Chlorine binding site 8 out of 24 in the Kshv Lana (ORF73) C-Terminal Domain, Decameric Ring: Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Kshv Lana (ORF73) C-Terminal Domain, Decameric Ring: Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl2150

b:87.1
occ:1.00
 NH2 C:ARG1119 3.5 49.3 1.0
CA C:GLY1067 3.7 56.0 1.0
N C:GLY1130 3.7 59.2 1.0
CB C:ALA1129 3.8 59.6 1.0
CA C:ALA1129 3.8 63.3 1.0
O C:GLY1067 4.2 56.4 1.0
C C:ALA1129 4.3 62.0 1.0
C C:GLY1067 4.3 55.0 1.0
NH1 C:ARG1119 4.3 49.9 1.0
CZ C:ARG1119 4.4 49.1 1.0
CE C:LYS1070 4.6 70.1 1.0
NZ C:LYS1070 4.8 72.7 1.0
CA C:GLY1130 4.8 60.9 1.0
N C:GLY1067 4.9 56.0 1.0

Chlorine binding site 9 out of 24 in 2ypy

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Chlorine binding site 9 out of 24 in the Kshv Lana (ORF73) C-Terminal Domain, Decameric Ring: Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Kshv Lana (ORF73) C-Terminal Domain, Decameric Ring: Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl2149

b:40.3
occ:0.74
 N D:ILE1136 3.2 37.8 1.0
NE2 D:GLN1116 3.4 58.0 1.0
OE1 D:GLN1116 3.5 55.7 1.0
CA D:SER1135 3.6 40.5 1.0
CG C:LYS1141 3.6 52.7 1.0
CD C:LYS1141 3.7 56.6 1.0
CD C:LYS1140 3.8 58.7 1.0
CG2 D:ILE1136 3.8 36.5 1.0
CD D:GLN1116 3.8 55.1 1.0
C D:SER1135 3.9 39.5 1.0
CG1 D:ILE1136 3.9 37.9 1.0
CB C:LYS1140 4.1 49.9 1.0
OG D:SER1135 4.2 48.3 1.0
CB D:ILE1136 4.2 35.9 1.0
CG C:LYS1140 4.3 55.3 1.0
CA D:ILE1136 4.3 37.0 1.0
CB D:SER1135 4.4 43.5 1.0
O D:SER1134 4.5 47.9 1.0
N D:SER1135 4.6 40.8 1.0
CD1 D:ILE1136 4.7 42.3 1.0
CE C:LYS1140 4.8 65.5 1.0
CB C:LYS1141 4.8 48.0 1.0
C D:SER1134 4.9 42.8 1.0
N C:LYS1141 4.9 46.3 1.0

Chlorine binding site 10 out of 24 in 2ypy

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Chlorine binding site 10 out of 24 in the Kshv Lana (ORF73) C-Terminal Domain, Decameric Ring: Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Kshv Lana (ORF73) C-Terminal Domain, Decameric Ring: Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl2150

b:75.4
occ:1.00
 NE2 E:HIS1126 3.7 54.1 1.0
CZ3 E:TRP1122 3.9 52.6 1.0
CA D:SER1125 4.0 59.9 1.0
CB D:SER1125 4.0 60.4 1.0
OG D:SER1125 4.1 62.0 1.0
O D:SER1125 4.3 59.7 1.0
CD1 E:PHE1037 4.3 42.7 1.0
CE1 E:HIS1126 4.3 57.1 1.0
CE3 E:TRP1122 4.4 49.8 1.0
CB E:PHE1037 4.5 41.2 1.0
CG E:PHE1037 4.6 41.3 1.0
C D:SER1125 4.6 58.9 1.0
CB E:SER1125 4.7 61.7 1.0
CD2 E:HIS1126 4.8 54.5 1.0
CH2 E:TRP1122 4.8 53.5 1.0
OG E:SER1125 4.9 62.9 1.0

Reference:

J.Hellert, M.Weidner-Glunde, J.Krausze, U.Richter, H.Adler, R.Fedorov, M.Pietrek, J.Ruckert, C.Ritter, T.F.Schulz, T.Luhrs. A Structural Basis For BRD2/4-Mediated Host Chromatin Interaction and Oligomer Assembly of Kaposi Sarcoma- Associated Herpesvirus and Murine Gammaherpesvirus Lana Proteins. Plos Pathog. V. 9 3640 2013.
ISSN: ISSN 1553-7366
PubMed: 24146614
DOI: 10.1371/JOURNAL.PPAT.1003640
Page generated: Sat Dec 12 09:29:46 2020

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