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Chlorine in PDB 4xdp: Crystal Structure of Human KDM4C Catalytic Domain Bound to Tris

Protein crystallography data

The structure of Crystal Structure of Human KDM4C Catalytic Domain Bound to Tris, PDB code: 4xdp was solved by K.K.Swinger, P.A.Boriack-Sjodin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.42 / 2.07
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 93.870, 89.750, 98.280, 90.00, 96.31, 90.00
R / Rfree (%) 20.7 / 24.2

Other elements in 4xdp:

The structure of Crystal Structure of Human KDM4C Catalytic Domain Bound to Tris also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Zinc (Zn) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human KDM4C Catalytic Domain Bound to Tris (pdb code 4xdp). 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 Human KDM4C Catalytic Domain Bound to Tris, PDB code: 4xdp:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4xdp

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Chlorine binding site 1 out of 6 in the Crystal Structure of Human KDM4C Catalytic Domain Bound to Tris


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 Human KDM4C Catalytic Domain Bound to Tris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:22.2
occ:1.00
 O A:HOH583 3.0 17.5 1.0
NH1 A:ARG324 3.1 24.8 0.5
O B:HOH535 3.2 9.3 1.0
NE A:ARG324 3.3 24.4 0.5
N B:TYR113 3.3 16.9 1.0
NZ A:LYS325 3.4 23.1 1.0
O B:TYR113 3.5 17.4 1.0
CG A:ARG324 3.5 23.2 0.5
CA B:ARG112 3.5 17.3 1.0
CD A:ARG324 3.8 24.5 0.5
CD A:LYS325 3.8 21.1 1.0
CG A:ARG324 3.8 23.4 0.5
CD A:ARG324 3.8 24.5 0.5
CE A:LYS325 3.9 22.1 1.0
C B:ARG112 3.9 16.9 1.0
CB B:ARG112 4.0 17.6 1.0
CZ A:ARG324 4.2 24.5 0.5
CD1 B:TYR113 4.3 16.8 1.0
CZ A:ARG324 4.3 24.3 0.5
C B:TYR113 4.4 17.1 1.0
NE A:ARG324 4.4 24.3 0.5
CA B:TYR113 4.4 16.6 1.0
NH2 A:ARG324 4.5 24.4 0.5
CE1 B:TYR113 4.5 17.1 1.0
O A:ARG324 4.5 21.2 0.5
O A:ARG324 4.5 21.2 0.5
CG B:ARG112 4.6 18.4 1.0
O B:PRO111 4.7 16.7 1.0
N B:ARG112 4.7 17.4 1.0
CG B:TYR113 4.8 16.3 1.0
C A:ARG324 4.8 20.8 0.5
C A:ARG324 4.8 20.8 0.5
CG A:LYS325 4.9 20.2 1.0
CB A:ARG324 4.9 22.3 0.5
CB A:ARG324 4.9 22.3 0.5

Chlorine binding site 2 out of 6 in 4xdp

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Chlorine binding site 2 out of 6 in the Crystal Structure of Human KDM4C Catalytic Domain Bound to Tris


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 Human KDM4C Catalytic Domain Bound to Tris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:24.2
occ:1.00
 N A:ARG112 3.4 18.2 1.0
CA A:PRO111 3.7 16.9 1.0
CG A:ARG112 3.9 20.4 1.0
CB A:PRO111 3.9 16.5 1.0
C A:PRO111 4.0 17.4 1.0
CB A:ARG112 4.2 20.0 1.0
CA A:ARG112 4.4 19.2 1.0
CD A:ARG112 4.7 21.6 1.0

Chlorine binding site 3 out of 6 in 4xdp

Go back to Chlorine Binding Sites List in 4xdp
Chlorine binding site 3 out of 6 in the Crystal Structure of Human KDM4C Catalytic Domain Bound to Tris


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 Human KDM4C Catalytic Domain Bound to Tris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:14.2
occ:1.00
 O A:HOH506 3.2 20.8 1.0
NE1 A:TRP183 3.2 14.2 1.0
CB A:ASN126 3.7 15.7 1.0
CG A:ASN126 3.7 16.3 1.0
CE2 A:TRP183 3.9 13.8 1.0
CZ2 A:TRP183 3.9 13.8 1.0
ND2 A:ASN126 4.0 16.2 1.0
OD1 A:ASN126 4.0 16.9 1.0
CB A:PRO111 4.2 16.5 1.0
CG A:PRO111 4.2 16.0 1.0
CD A:PRO111 4.3 15.8 1.0
CD1 A:TRP183 4.3 14.3 1.0
CD A:LYS184 4.7 15.6 1.0
O A:HOH543 4.9 14.1 1.0
O A:LYS122 4.9 16.0 1.0

Chlorine binding site 4 out of 6 in 4xdp

Go back to Chlorine Binding Sites List in 4xdp
Chlorine binding site 4 out of 6 in the Crystal Structure of Human KDM4C Catalytic Domain Bound to Tris


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 Human KDM4C Catalytic Domain Bound to Tris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl410

b:25.2
occ:1.00
 O A:HOH551 2.9 18.0 1.0
O A:HOH615 3.2 25.0 1.0
N A:VAL296 3.4 16.6 1.0
CA A:THR295 3.7 15.8 1.0
CG2 A:VAL296 3.7 18.4 1.0
CB A:THR295 3.8 15.6 1.0
CG1 A:VAL158 3.8 18.6 1.0
C A:THR295 4.0 16.0 1.0
CB A:VAL296 4.2 18.1 1.0
CG2 A:THR295 4.4 15.5 1.0
O A:HOH590 4.4 21.9 1.0
CA A:VAL296 4.4 17.2 1.0
O A:HOH513 4.9 18.6 1.0

Chlorine binding site 5 out of 6 in 4xdp

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Chlorine binding site 5 out of 6 in the Crystal Structure of Human KDM4C Catalytic Domain Bound to Tris


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 Human KDM4C Catalytic Domain Bound to Tris within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl405

b:27.0
occ:1.00
 NH2 B:ARG324 2.9 39.0 0.5
NZ B:LYS325 3.2 39.0 1.0
NE B:ARG324 3.3 38.3 0.5
CG B:ARG324 3.4 35.9 0.5
CG B:ARG324 3.6 35.8 0.5
CE B:LYS325 3.7 37.5 1.0
CD B:ARG324 3.8 37.4 0.5
CD B:LYS325 3.8 35.6 1.0
CD B:ARG324 3.9 37.5 0.5
CZ B:ARG324 4.1 38.6 0.5
CZ B:ARG324 4.3 38.1 0.5
NE B:ARG324 4.4 37.9 0.5
NH2 B:ARG324 4.5 39.2 0.5
O B:ARG324 4.5 33.2 0.5
O B:ARG324 4.5 33.1 0.5
C B:ARG324 4.8 32.7 0.5
C B:ARG324 4.8 32.7 0.5
CB B:ARG324 4.8 34.1 0.5
CB B:ARG324 4.8 34.2 0.5
CG B:LYS325 4.9 34.2 1.0

Chlorine binding site 6 out of 6 in 4xdp

Go back to Chlorine Binding Sites List in 4xdp
Chlorine binding site 6 out of 6 in the Crystal Structure of Human KDM4C Catalytic Domain Bound to Tris


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 Human KDM4C Catalytic Domain Bound to Tris within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl406

b:16.5
occ:1.00
 O B:HOH523 3.0 28.6 1.0
NE1 B:TRP183 3.2 18.2 1.0
O B:HOH516 3.2 25.4 1.0
CB B:ASN126 3.7 19.2 1.0
CG B:ASN126 3.7 19.3 1.0
CE2 B:TRP183 3.8 17.4 1.0
CZ2 B:TRP183 3.9 16.9 1.0
O B:HOH512 4.0 17.2 1.0
ND2 B:ASN126 4.0 18.6 1.0
OD1 B:ASN126 4.1 20.2 1.0
CB B:PRO111 4.2 17.1 1.0
CG B:PRO111 4.2 16.5 1.0
CD1 B:TRP183 4.3 18.8 1.0
CD B:PRO111 4.3 16.9 1.0
CD B:LYS184 4.8 20.5 1.0
O B:LYS122 4.8 17.7 0.5
O B:LYS122 4.8 17.7 0.5
O B:HOH518 5.0 19.9 1.0

Reference:

T.J.Wigle, K.K.Swinger, J.E.Campbell, M.D.Scholle, J.Sherrill, E.A.Admirand, P.A.Boriack-Sjodin, K.W.Kuntz, R.Chesworth, M.P.Moyer, M.P.Scott, R.A.Copeland. A High-Throughput Mass Spectrometry Assay Coupled with Redox Activity Testing Reduces Artifacts and False Positives in Lysine Demethylase Screening. J Biomol Screen 2015.
ISSN: ESSN 1552-454X
PubMed: 25755264
DOI: 10.1177/1087057115575689
Page generated: Fri Jul 26 03:23:09 2024

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