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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

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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

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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

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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

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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

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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

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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

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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

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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

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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: Tue Jul 30 18:40:09 2024

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