Magnesium in PDB 8sq9: Sars-Cov-2 Replication-Transcription Complex Bound to NSP9 and Umpcpp, As A Pre-Catalytic Nmpylation Intermediate

Enzymatic activity of Sars-Cov-2 Replication-Transcription Complex Bound to NSP9 and Umpcpp, As A Pre-Catalytic Nmpylation Intermediate

All present enzymatic activity of Sars-Cov-2 Replication-Transcription Complex Bound to NSP9 and Umpcpp, As A Pre-Catalytic Nmpylation Intermediate:
2.7.7.48;

Other elements in 8sq9:

The structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP9 and Umpcpp, As A Pre-Catalytic Nmpylation Intermediate also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP9 and Umpcpp, As A Pre-Catalytic Nmpylation Intermediate (pdb code 8sq9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP9 and Umpcpp, As A Pre-Catalytic Nmpylation Intermediate, PDB code: 8sq9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8sq9

Go back to Magnesium Binding Sites List in 8sq9
Magnesium binding site 1 out of 4 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP9 and Umpcpp, As A Pre-Catalytic Nmpylation Intermediate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sars-Cov-2 Replication-Transcription Complex Bound to NSP9 and Umpcpp, As A Pre-Catalytic Nmpylation Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:83.3
occ:1.00
 OD2 A:ASP618 1.9 87.9 1.0
OD1 A:ASP761 2.5 82.1 1.0
O3' P:A35 2.9 80.0 1.0
CG A:ASP618 2.9 86.9 1.0
HO3' P:A35 3.0 79.0 1.0
OD1 A:ASP760 3.3 81.1 1.0
O2A A:WSB1005 3.3 84.5 1.0
O A:HOH1277 3.3 79.3 1.0
OD1 A:ASP618 3.3 86.3 1.0
OD2 A:ASP760 3.7 83.5 1.0
CG A:ASP761 3.7 83.5 1.0
CG A:ASP760 3.8 81.1 1.0
O5' P:A35 4.1 83.9 1.0
C3' P:A35 4.2 76.1 1.0
CB A:ASP618 4.2 82.8 1.0
HB2 A:ASP618 4.3 81.0 1.0
PA A:WSB1005 4.3 84.7 1.0
H3' P:A35 4.4 78.4 1.0
O1A A:WSB1005 4.4 84.8 1.0
HB2 A:ASP761 4.4 74.4 1.0
HA A:ASP761 4.5 75.0 1.0
MG A:MG1004 4.5 71.8 1.0
CB A:ASP761 4.6 73.8 1.0
OD2 A:ASP761 4.6 84.6 1.0
H4' P:A35 4.7 77.9 1.0
HB3 A:ASP618 4.8 80.8 1.0
C4' P:A35 4.8 78.7 1.0
N A:ASP761 4.9 74.3 1.0
CA A:ASP761 4.9 71.1 1.0
C5' P:A35 4.9 82.3 1.0
HA A:ASP618 4.9 80.3 1.0
H5'' P:A35 4.9 78.7 1.0
OP1 P:A35 5.0 82.6 1.0
C A:ASP760 5.0 80.2 1.0

Magnesium binding site 2 out of 4 in 8sq9

Go back to Magnesium Binding Sites List in 8sq9
Magnesium binding site 2 out of 4 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP9 and Umpcpp, As A Pre-Catalytic Nmpylation Intermediate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Sars-Cov-2 Replication-Transcription Complex Bound to NSP9 and Umpcpp, As A Pre-Catalytic Nmpylation Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1004

b:71.8
occ:1.00
 O1B A:WSB1005 2.0 84.7 1.0
OD1 A:ASP618 2.1 86.3 1.0
O A:TYR619 2.1 78.5 1.0
OD2 A:ASP760 2.8 83.5 1.0
O2A A:WSB1005 2.8 84.5 1.0
O3G A:WSB1005 2.8 84.8 1.0
HZ3 A:LYS798 3.2 88.2 1.0
CG A:ASP618 3.3 86.9 1.0
C A:TYR619 3.3 76.4 1.0
PB A:WSB1005 3.4 84.9 1.0
HZ1 A:LYS798 3.6 88.7 1.0
N A:TYR619 3.7 74.5 1.0
NZ A:LYS798 3.8 89.2 1.0
HB2 A:CYS622 3.9 86.6 1.0
O A:PRO620 4.0 87.9 1.0
O3B A:WSB1005 4.0 85.0 1.0
HB2 A:TYR619 4.0 73.3 1.0
CA A:TYR619 4.0 73.8 1.0
OD2 A:ASP618 4.0 87.9 1.0
CG A:ASP760 4.0 81.1 1.0
PA A:WSB1005 4.0 84.7 1.0
PG A:WSB1005 4.0 84.9 1.0
H A:CYS622 4.1 87.2 1.0
C A:ASP618 4.2 85.7 1.0
C3A A:WSB1005 4.2 85.0 1.0
HB3 A:ASP618 4.2 80.8 1.0
HZ2 A:LYS798 4.3 89.0 1.0
CB A:ASP618 4.3 82.8 1.0
C A:PRO620 4.3 85.7 1.0
HA A:PRO620 4.3 80.5 1.0
C5' A:WSB1005 4.3 84.5 1.0
N A:PRO620 4.4 74.1 1.0
CA A:PRO620 4.5 80.5 1.0
MG A:MG1003 4.5 83.3 1.0
CB A:TYR619 4.6 70.5 1.0
O2B A:WSB1005 4.6 85.0 1.0
HB3 A:CYS622 4.7 87.5 1.0
CA A:ASP618 4.7 84.9 1.0
HB2 A:ASP760 4.7 76.2 1.0
CB A:CYS622 4.7 85.3 1.0
O A:ASP618 4.7 81.9 1.0
HA A:ASP618 4.7 80.3 1.0
O5' A:WSB1005 4.7 84.6 1.0
N A:CYS622 4.8 85.0 1.0
OD1 A:ASP760 4.8 81.1 1.0
O1G A:WSB1005 4.9 85.1 1.0
HA A:TYR619 4.9 73.3 1.0
HE2 A:LYS798 4.9 88.5 1.0
CB A:ASP760 5.0 72.8 1.0

Magnesium binding site 3 out of 4 in 8sq9

Go back to Magnesium Binding Sites List in 8sq9
Magnesium binding site 3 out of 4 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP9 and Umpcpp, As A Pre-Catalytic Nmpylation Intermediate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Sars-Cov-2 Replication-Transcription Complex Bound to NSP9 and Umpcpp, As A Pre-Catalytic Nmpylation Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1006

b:76.8
occ:1.00
 HE1 A:HIS75 2.4 73.3 1.0
HH21 A:ARG116 2.4 75.1 1.0
HE2 A:HIS75 2.5 73.6 1.0
CE1 A:HIS75 2.9 75.4 1.0
OD2 A:ASP218 2.9 75.7 1.0
O2B A:WSB1008 3.0 103.6 1.0
NE2 A:HIS75 3.0 78.3 1.0
NH2 A:ARG116 3.0 85.8 1.0
HH22 A:ARG116 3.1 75.4 1.0
HZ2 A:LYS73 3.3 81.3 0.5
HD2 A:LYS73 3.6 82.0 0.5
PB A:WSB1008 3.7 118.0 1.0
OE2 A:GLU83 3.7 75.5 1.0
O1B A:WSB1008 3.7 103.1 1.0
CG A:ASP218 3.9 76.3 1.0
O3B A:WSB1008 4.1 107.6 1.0
HE2 A:LYS73 4.1 81.1 0.5
HE3 A:LYS73 4.2 81.2 0.5
ND1 A:HIS75 4.2 75.4 1.0
CZ A:ARG116 4.2 83.3 1.0
HE A:ARG116 4.3 73.8 1.0
NZ A:LYS73 4.3 80.0 0.5
CD2 A:HIS75 4.3 73.5 1.0
CD A:LYS73 4.4 84.4 0.5
OD1 A:ASP218 4.5 76.2 1.0
HD3 A:LYS73 4.5 81.5 0.5
O A:HOH1280 4.5 79.6 1.0
O A:HOH1142 4.6 62.9 1.0
CE A:LYS73 4.6 83.6 0.5
HZ1 A:LYS73 4.6 80.6 0.5
HG3 A:LYS73 4.6 81.0 0.5
CD A:GLU83 4.6 79.5 1.0
OE1 A:GLU83 4.7 79.0 1.0
NE A:ARG116 4.7 70.6 1.0
HZ3 A:LYS73 4.7 80.6 0.5
HB2 A:ASP218 4.9 68.2 1.0
O3G A:WSB1008 4.9 99.1 1.0
HD2 A:HIS75 4.9 72.4 1.0
HA A:ASP218 4.9 66.9 1.0
CG A:HIS75 5.0 72.0 1.0
CE A:LYS73 5.0 81.2 0.5
CB A:ASP218 5.0 71.4 1.0

Magnesium binding site 4 out of 4 in 8sq9

Go back to Magnesium Binding Sites List in 8sq9
Magnesium binding site 4 out of 4 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP9 and Umpcpp, As A Pre-Catalytic Nmpylation Intermediate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Sars-Cov-2 Replication-Transcription Complex Bound to NSP9 and Umpcpp, As A Pre-Catalytic Nmpylation Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1007

b:87.1
occ:1.00
 H2 G:ASN1 1.7 70.3 1.0
N G:ASN1 2.1 76.4 1.0
H3 G:ASN1 2.2 69.7 1.0
H1 G:ASN1 2.2 71.7 1.0
OD2 A:ASP208 2.5 64.8 1.0
O2A A:WSB1008 2.6 98.8 1.0
HD1 A:PHE35 3.1 65.1 1.0
HB3 A:PHE35 3.5 63.5 1.0
CA G:ASN1 3.5 67.4 1.0
CG A:ASP208 3.6 70.2 1.0
O1G A:WSB1008 3.7 100.9 1.0
HA G:ASN1 3.8 68.6 1.0
CD1 A:PHE35 3.9 65.9 1.0
PA A:WSB1008 3.9 109.8 1.0
O A:ASP36 4.0 65.7 1.0
H A:ASP36 4.1 66.2 1.0
HA A:ILE37 4.1 64.7 1.0
OD1 A:ASP208 4.2 76.2 1.0
C G:ASN1 4.2 63.7 1.0
H G:ASN2 4.3 64.6 1.0
CB A:PHE35 4.4 51.4 1.0
HG13 A:ILE37 4.4 64.3 1.0
HB A:ILE37 4.5 63.5 1.0
N G:ASN2 4.5 62.7 1.0
O1A A:WSB1008 4.5 102.2 1.0
HB2 G:ASN1 4.5 69.9 1.0
O5' A:WSB1008 4.5 105.6 1.0
CB G:ASN1 4.6 65.5 1.0
C A:ASP36 4.6 61.5 1.0
HD21 A:ASN209 4.6 66.8 1.0
CG A:PHE35 4.6 51.8 1.0
C5' A:WSB1008 4.7 98.3 1.0
N A:ASP36 4.7 67.8 1.0
HB2 A:ASP208 4.7 62.3 1.0
HB3 G:ASN1 4.7 68.7 1.0
HE1 A:PHE35 4.7 64.6 1.0
HB2 G:ASN2 4.8 61.5 1.0
CE1 A:PHE35 4.8 71.3 1.0
CB A:ASP208 4.8 59.8 1.0
OG1 A:THR206 4.8 53.2 1.0
HA A:PHE35 4.8 64.0 1.0
CA A:ILE37 4.9 61.1 1.0
HG1 A:THR206 4.9 61.2 1.0
O G:ASN1 4.9 69.8 1.0
HG21 A:THR206 5.0 62.1 1.0

Reference:

G.I.Small, O.Fedorova, P.D.B.Olinares, J.Chandanani, A.Banerjee, Y.J.Choi, H.Molina, B.T.Chait, S.A.Darst, E.A.Campbell. Structural and Functional Insights Into the Enzymatic Plasticity of the Sars-Cov-2 Niran Domain. Mol.Cell V. 83 3921 2023.
ISSN: ISSN 1097-2765
PubMed: 37890482
DOI: 10.1016/J.MOLCEL.2023.10.001
Page generated: Fri Oct 4 19:58:35 2024

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