Atomistry » Cobalt » PDB 6ega-6kdc » 6izx
Atomistry »
  Cobalt »
    PDB 6ega-6kdc »
      6izx »

Cobalt in PDB 6izx: The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5, Bound with Rk-0404678

Protein crystallography data

The structure of The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5, Bound with Rk-0404678, PDB code: 6izx was solved by H.Shimizu, S.Sekine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.74 / 2.43
Space group I 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 236.500, 236.500, 236.500, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 23.1

Other elements in 6izx:

The structure of The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5, Bound with Rk-0404678 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5, Bound with Rk-0404678 (pdb code 6izx). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 9 binding sites of Cobalt where determined in the The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5, Bound with Rk-0404678, PDB code: 6izx:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cobalt binding site 1 out of 9 in 6izx

Go back to Cobalt Binding Sites List in 6izx
Cobalt binding site 1 out of 9 in the The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5, Bound with Rk-0404678


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5, Bound with Rk-0404678 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co903

b:62.7
occ:1.00
 O A:HOH1047 1.9 37.0 1.0
O A:HOH1036 1.9 64.5 1.0
O A:HOH1195 2.8 58.8 1.0
O A:HOH1189 3.0 56.0 1.0
OG1 A:THR606 3.4 39.2 1.0
N A:GLY608 3.8 44.2 1.0
OG1 A:THR611 3.9 35.1 1.0
CA A:GLY608 3.9 37.4 1.0
O A:HOH1186 4.0 50.1 1.0
N A:THR606 4.0 51.6 1.0
CB A:ASN610 4.2 34.0 1.0
CA A:GLY662 4.2 32.8 1.0
N A:THR611 4.3 28.0 1.0
C A:GLY608 4.4 39.0 1.0
CB A:THR606 4.5 44.8 1.0
N A:GLY662 4.5 33.4 1.0
N A:ASN610 4.5 33.2 1.0
CA A:THR606 4.6 42.4 1.0
C A:THR606 4.7 44.9 1.0
N A:LEU609 4.7 35.9 1.0
CB A:THR611 4.8 30.4 1.0
N A:TYR607 4.8 49.5 1.0
CA A:ASN610 4.8 32.6 1.0
CG2 A:THR606 4.9 44.5 1.0
O A:GLY608 5.0 35.2 1.0

Cobalt binding site 2 out of 9 in 6izx

Go back to Cobalt Binding Sites List in 6izx
Cobalt binding site 2 out of 9 in the The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5, Bound with Rk-0404678


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5, Bound with Rk-0404678 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co904

b:89.1
occ:1.00
 OG A:SER291 3.1 52.9 1.0
N A:SER291 3.7 54.4 1.0
CA A:HIS288 3.8 53.2 1.0
CB A:SER291 3.9 52.0 1.0
CB A:THR290 3.9 58.8 1.0
CB A:HIS288 4.0 52.0 1.0
C A:HIS288 4.1 54.8 1.0
N A:THR290 4.3 53.0 1.0
O A:HIS288 4.3 50.7 1.0
CA A:SER291 4.4 50.3 1.0
CA A:THR290 4.4 55.0 1.0
C A:THR290 4.5 56.5 1.0
CD2 A:HIS288 4.5 51.6 1.0
OG1 A:THR290 4.6 62.9 1.0
CG A:HIS288 4.6 54.4 1.0
CG2 A:THR290 4.8 57.3 1.0
N A:GLU289 4.9 54.4 1.0
O A:GLU287 5.0 54.0 1.0

Cobalt binding site 3 out of 9 in 6izx

Go back to Cobalt Binding Sites List in 6izx
Cobalt binding site 3 out of 9 in the The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5, Bound with Rk-0404678


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5, Bound with Rk-0404678 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co905

b:0.6
occ:1.00
 O A:HOH1188 2.6 65.6 1.0
NZ A:LYS548 2.9 61.5 1.0
NH1 A:ARG596 3.5 46.8 1.0
NH2 A:ARG596 3.7 48.8 1.0
CE A:LYS548 3.9 51.8 1.0
CZ A:ARG596 4.1 49.1 1.0
CD2 A:LEU544 4.7 40.3 1.0

Cobalt binding site 4 out of 9 in 6izx

Go back to Cobalt Binding Sites List in 6izx
Cobalt binding site 4 out of 9 in the The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5, Bound with Rk-0404678


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5, Bound with Rk-0404678 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co906

b:85.5
occ:1.00
 O A:HOH1184 3.7 56.8 1.0
NH1 A:ARG654 3.8 38.7 1.0
NH2 A:ARG654 3.8 49.9 1.0
CG1 A:VAL650 4.1 45.8 1.0
NH2 A:ARG649 4.2 70.4 1.0
CZ A:ARG654 4.3 44.7 1.0
CD1 A:LEU670 4.5 44.9 1.0

Cobalt binding site 5 out of 9 in 6izx

Go back to Cobalt Binding Sites List in 6izx
Cobalt binding site 5 out of 9 in the The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5, Bound with Rk-0404678


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5, Bound with Rk-0404678 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co907

b:96.0
occ:1.00
 N A:GLY537 3.4 38.2 1.0
NZ A:LYS689 3.9 79.1 1.0
CA A:GLY537 4.0 30.6 1.0
NZ A:LYS358 4.3 71.1 1.0
CE A:LYS689 4.3 66.6 1.0
C A:ALA536 4.4 36.7 1.0
CA A:ALA536 4.6 37.6 1.0
CD A:LYS689 4.7 56.3 1.0
O A:HOH1042 4.8 45.2 1.0
O A:THR535 5.0 41.4 1.0

Cobalt binding site 6 out of 9 in 6izx

Go back to Cobalt Binding Sites List in 6izx
Cobalt binding site 6 out of 9 in the The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5, Bound with Rk-0404678


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5, Bound with Rk-0404678 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co908

b:0.1
occ:1.00
 O A:HOH1041 3.2 54.7 1.0
OG1 A:THR311 3.3 56.8 1.0
NE2 A:HIS288 4.1 47.9 1.0
CB A:THR311 4.1 53.7 1.0
CE1 A:TYR309 4.1 43.6 1.0
CA A:THR311 4.2 54.6 1.0
O A:GLU310 4.4 51.0 1.0
CD2 A:HIS288 4.5 51.6 1.0
N A:LYS312 4.6 57.0 1.0
CD1 A:TYR309 4.8 48.1 1.0
OH A:TYR309 4.9 49.7 1.0

Cobalt binding site 7 out of 9 in 6izx

Go back to Cobalt Binding Sites List in 6izx
Cobalt binding site 7 out of 9 in the The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5, Bound with Rk-0404678


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5, Bound with Rk-0404678 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co909

b:0.5
occ:1.00
 NE1 A:TRP803 3.4 46.5 1.0
CE2 A:TRP803 4.1 47.8 1.0
CZ2 A:TRP803 4.2 50.7 1.0
CE A:MET761 4.2 40.3 1.0
OG A:SER757 4.3 57.0 1.0
CD1 A:TRP803 4.4 47.6 1.0
CE1 A:TYR758 4.7 41.3 1.0
CG A:MET761 4.8 40.3 1.0
O A:SER757 4.8 30.6 1.0
CZ A:TYR758 4.9 45.2 1.0
CD1 A:TYR758 4.9 34.3 1.0
CB A:MET761 4.9 35.9 1.0
CB A:SER757 4.9 39.0 1.0
C A:SER757 5.0 33.9 1.0
NH2 A:ARG737 5.0 74.0 1.0

Cobalt binding site 8 out of 9 in 6izx

Go back to Cobalt Binding Sites List in 6izx
Cobalt binding site 8 out of 9 in the The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5, Bound with Rk-0404678


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5, Bound with Rk-0404678 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co910

b:0.5
occ:1.00
 NE1 A:TRP823 3.6 41.6 1.0
CD1 A:TRP823 4.0 42.1 1.0
CE2 A:TRP823 4.0 40.9 1.0
CB A:PRO822 4.3 39.7 1.0
O A:PRO822 4.3 47.7 1.0
CZ2 A:TRP823 4.5 37.7 1.0
O A:HOH1136 4.5 48.6 1.0
CG A:TRP823 4.5 43.3 1.0
CD2 A:TRP823 4.6 41.4 1.0
C A:PRO822 4.7 42.5 1.0
OD2 A:ASP521 4.9 45.3 1.0

Cobalt binding site 9 out of 9 in 6izx

Go back to Cobalt Binding Sites List in 6izx
Cobalt binding site 9 out of 9 in the The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5, Bound with Rk-0404678


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of The Rna-Dependent Rna Polymerase Domain of Dengue 2 NS5, Bound with Rk-0404678 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co911

b:0.4
occ:1.00
 N A:GLY559 3.3 59.8 1.0
CA A:GLU558 4.0 59.8 1.0
CA A:GLY559 4.1 55.0 1.0
CB A:GLU558 4.1 63.4 1.0
C A:GLU558 4.1 60.0 1.0
O A:GLY559 4.9 51.8 1.0

Reference:

H.Shimizu, S.Sekine. Rk-0404678 Bound Form of DENV2 Rdrp To Be Published.
Page generated: Sun Dec 13 10:50:21 2020

Last articles

Cl in 6COG
Cl in 6CST
Cl in 6CTW
Cl in 6CTZ
Cl in 6CTT
Cl in 6CSP
Cl in 6CU9
Cl in 6CTX
Cl in 6CTU
Cl in 6CTP
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy