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Nickel in PDB 8dcb: Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with NI2+ and Gtp

Enzymatic activity of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with NI2+ and Gtp

All present enzymatic activity of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with NI2+ and Gtp:
6.5.1.8;

Protein crystallography data

The structure of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with NI2+ and Gtp, PDB code: 8dcb was solved by A.Jacewicz, S.Dantuluri, S.Shuman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.52 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.241, 137.492, 149.559, 90, 90, 90
R / Rfree (%) 17 / 20.9

Other elements in 8dcb:

The structure of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with NI2+ and Gtp also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with NI2+ and Gtp (pdb code 8dcb). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 5 binding sites of Nickel where determined in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with NI2+ and Gtp, PDB code: 8dcb:
Jump to Nickel binding site number: 1; 2; 3; 4; 5;

Nickel binding site 1 out of 5 in 8dcb

Go back to Nickel Binding Sites List in 8dcb
Nickel binding site 1 out of 5 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with NI2+ and Gtp


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with NI2+ and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni503

b:73.3
occ:0.90
 NE2 A:HIS234 2.3 52.3 1.0
NE2 A:HIS329 2.3 55.9 1.0
O A:HOH602 2.3 62.7 1.0
SG A:CYS98 2.5 64.5 1.0
O2A A:GTP501 2.6 70.8 0.7
O1B A:GTP501 2.8 57.2 1.0
CE1 A:HIS234 3.0 52.1 1.0
O5' A:GTP501 3.1 70.7 1.0
CD2 A:HIS329 3.2 63.5 1.0
CE1 A:HIS329 3.3 54.3 1.0
NI A:NI504 3.3 69.0 0.6
PA A:GTP501 3.4 65.1 0.6
CD2 A:HIS234 3.4 58.1 1.0
CB A:CYS98 3.6 55.0 1.0
PB A:GTP501 3.7 80.2 1.0
O3A A:GTP501 3.9 72.2 0.0
O3B A:GTP501 4.2 70.9 0.0
ND1 A:HIS234 4.2 61.7 1.0
C5' A:GTP501 4.3 70.9 0.0
O1G A:GTP501 4.4 64.5 1.0
ND1 A:HIS329 4.4 62.3 1.0
CG A:HIS329 4.4 58.8 1.0
CG A:HIS234 4.5 53.2 1.0
CD2 A:HIS404 4.5 62.2 1.0
C A:CYS98 4.6 52.5 1.0
O2G A:GTP501 4.6 70.8 0.9
PG A:GTP501 4.7 69.6 0.6
CA A:CYS98 4.7 59.8 1.0
NE2 A:HIS404 4.8 71.6 1.0
O1A A:GTP501 4.8 78.2 1.0
ND2 A:ASN330 4.8 58.4 1.0
N A:GLY99 4.8 51.1 1.0
O A:CYS98 4.8 55.8 1.0
NE2 A:HIS203 4.9 69.7 1.0
CD2 A:HIS203 4.9 56.0 1.0

Nickel binding site 2 out of 5 in 8dcb

Go back to Nickel Binding Sites List in 8dcb
Nickel binding site 2 out of 5 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with NI2+ and Gtp


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with NI2+ and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni504

b:69.0
occ:0.60
 OD2 A:ASP95 2.2 66.8 1.0
O2G A:GTP501 2.2 70.8 0.9
NE2 A:HIS203 2.2 69.7 1.0
O1B A:GTP501 2.3 57.2 1.0
SG A:CYS98 2.4 64.5 1.0
CB A:CYS98 3.0 55.0 1.0
CD2 A:HIS203 3.1 56.0 1.0
CG A:ASP95 3.2 65.2 1.0
CE1 A:HIS203 3.3 58.2 1.0
PG A:GTP501 3.3 69.6 0.6
NI A:NI503 3.3 73.3 0.9
PB A:GTP501 3.5 80.2 1.0
O1G A:GTP501 3.5 64.5 1.0
CB A:ASP95 3.8 61.1 1.0
O3B A:GTP501 3.9 70.9 0.0
O A:HOH602 4.0 62.7 1.0
NE2 A:HIS234 4.0 52.3 1.0
OD1 A:ASP95 4.2 68.3 1.0
O2B A:GTP501 4.2 81.2 0.4
CG A:HIS203 4.3 60.8 1.0
ND1 A:HIS203 4.3 67.5 1.0
CA A:CYS98 4.3 59.8 1.0
O3G A:GTP501 4.6 65.2 0.7
CE1 A:HIS234 4.7 52.1 1.0
O2A A:GTP501 4.7 70.8 0.7
N A:GLY236 4.8 54.0 1.0
CD2 A:HIS234 4.8 58.1 1.0
O3A A:GTP501 4.8 72.2 0.0
ND2 A:ASN330 4.8 58.4 1.0
O2 A:SO4505 5.0 75.4 1.0
C A:THR235 5.0 55.1 1.0

Nickel binding site 3 out of 5 in 8dcb

Go back to Nickel Binding Sites List in 8dcb
Nickel binding site 3 out of 5 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with NI2+ and Gtp


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with NI2+ and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni502

b:73.4
occ:0.69
 O2G B:GTP501 2.2 60.9 1.0
SG B:CYS98 2.2 62.2 1.0
NE2 B:HIS203 2.2 62.1 1.0
O1B B:GTP501 2.4 53.4 0.6
OD2 B:ASP95 2.5 74.8 1.0
CB B:CYS98 2.9 52.1 1.0
CG B:ASP95 3.2 60.3 1.0
CE1 B:HIS203 3.2 65.9 1.0
CD2 B:HIS203 3.2 63.1 1.0
PG B:GTP501 3.3 53.6 0.5
O B:HOH601 3.5 58.2 1.0
PB B:GTP501 3.5 49.3 0.7
CB B:ASP95 3.6 52.0 1.0
NI B:NI503 3.6 76.1 0.9
O3G B:GTP501 3.6 55.6 0.7
O3B B:GTP501 3.8 59.1 0.7
O2B B:GTP501 4.0 66.1 0.7
OD1 B:ASP95 4.1 63.7 1.0
CA B:CYS98 4.2 53.0 1.0
ND1 B:HIS203 4.3 62.0 1.0
CG B:HIS203 4.4 66.1 1.0
NE2 B:HIS234 4.4 56.9 1.0
O2A B:GTP501 4.6 61.5 0.2
O1G B:GTP501 4.6 58.9 0.8
N B:GLY236 4.7 54.9 1.0
O3A B:GTP501 4.9 64.5 0.6
CA B:GLY236 4.9 52.9 1.0
C B:THR235 5.0 52.0 1.0

Nickel binding site 4 out of 5 in 8dcb

Go back to Nickel Binding Sites List in 8dcb
Nickel binding site 4 out of 5 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with NI2+ and Gtp


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with NI2+ and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni503

b:76.1
occ:0.94
 O2A B:GTP501 2.1 61.5 0.2
NE2 B:HIS329 2.2 54.1 1.0
O1B B:GTP501 2.3 53.4 0.6
O B:HOH601 2.3 58.2 1.0
NE2 B:HIS234 2.3 56.9 1.0
SG B:CYS98 2.6 62.2 1.0
PA B:GTP501 3.0 64.1 0.7
CE1 B:HIS329 3.1 49.8 1.0
CE1 B:HIS234 3.1 56.6 1.0
O5' B:GTP501 3.2 59.2 1.0
CD2 B:HIS329 3.3 54.7 1.0
PB B:GTP501 3.4 49.3 0.7
CD2 B:HIS234 3.5 52.7 1.0
O3A B:GTP501 3.5 64.5 0.6
NI B:NI502 3.6 73.4 0.7
CB B:CYS98 3.8 52.1 1.0
O3B B:GTP501 4.1 59.1 0.7
ND1 B:HIS329 4.2 58.5 1.0
ND1 B:HIS234 4.3 62.1 1.0
CG B:HIS329 4.3 52.1 1.0
C5' B:GTP501 4.4 69.6 0.4
O3G B:GTP501 4.4 55.6 0.7
O1A B:GTP501 4.4 69.1 1.0
CG B:HIS234 4.5 56.5 1.0
CD2 B:HIS404 4.6 69.6 1.0
O2B B:GTP501 4.6 66.1 0.7
PG B:GTP501 4.6 53.6 0.5
O2G B:GTP501 4.7 60.9 1.0
NE2 B:HIS404 4.7 71.8 1.0
CD2 B:HIS203 4.8 63.1 1.0
C B:CYS98 4.8 57.1 1.0
NE2 B:HIS203 4.8 62.1 1.0
CA B:CYS98 4.9 53.0 1.0
N B:GLY99 4.9 53.2 1.0

Nickel binding site 5 out of 5 in 8dcb

Go back to Nickel Binding Sites List in 8dcb
Nickel binding site 5 out of 5 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with NI2+ and Gtp


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with NI2+ and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni504

b:106.8
occ:0.65
 OE2 B:GLU305 2.8 106.7 1.0
NE2 B:HIS301 2.9 72.0 1.0
CD2 B:HIS301 3.7 65.2 1.0
CD B:GLU305 3.8 99.0 1.0
CE1 B:HIS301 3.9 67.5 1.0
OE1 B:GLU305 4.1 104.5 1.0
CG B:HIS301 4.9 70.2 1.0
O B:GLY159 4.9 76.1 1.0

Reference:

A.Jacewicz, S.Dantuluri, S.Shuman. Structures of Rna Ligase Rtcb in Complexes with Divalent Cations and Gtp. Rna V. 28 1509 2022.
ISSN: ESSN 1469-9001
PubMed: 36130078
DOI: 10.1261/RNA.079327.122
Page generated: Thu Oct 10 09:39:11 2024

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