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Magnesium in PDB 9ofc: Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three Intact Dimers

Enzymatic activity of Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three Intact Dimers

All present enzymatic activity of Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three Intact Dimers:
3.5.4.4;

Other elements in 9ofc:

The structure of Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three Intact Dimers also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three Intact Dimers (pdb code 9ofc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three Intact Dimers, PDB code: 9ofc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 9ofc

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Magnesium binding site 1 out of 8 in the Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three Intact Dimers


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three Intact Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg702

b:129.2
occ:1.00
 H2' G:ATP701 1.9 132.1 1.0
O2A G:ATP701 1.9 133.1 1.0
O5' G:ATP701 2.0 134.2 1.0
H8 G:ATP701 2.1 130.8 1.0
PA G:ATP701 2.4 136.3 1.0
C2' G:ATP701 2.8 134.2 1.0
H5'1 G:ATP701 2.9 131.2 1.0
C5' G:ATP701 2.9 134.7 1.0
C8 G:ATP701 3.0 130.5 1.0
O3A G:ATP701 3.1 133.4 1.0
H3' G:ATP701 3.4 131.7 1.0
C3' G:ATP701 3.4 133.0 1.0
O3B G:ATP701 3.6 139.8 1.0
C4' G:ATP701 3.6 135.2 1.0
C1' G:ATP701 3.6 136.1 1.0
N9 G:ATP701 3.7 132.2 1.0
O1A G:ATP701 3.7 132.7 1.0
H5'2 G:ATP701 3.7 131.2 1.0
O G:HOH2006 3.8 96.2 1.0
O2' G:ATP701 3.8 133.5 1.0
O4' G:ATP701 3.8 136.7 1.0
N7 G:ATP701 4.0 131.9 1.0
PB G:ATP701 4.1 141.5 1.0
O2G G:ATP701 4.1 133.1 1.0
O G:HOH2003 4.1 99.2 1.0
MG G:MG703 4.4 119.4 1.0
O G:HOH2002 4.5 110.3 1.0
HO2' G:ATP701 4.5 132.2 1.0
H4' G:ATP701 4.5 131.6 1.0
H1' G:ATP701 4.5 132.6 1.0
PG G:ATP701 4.6 146.1 1.0
CE G:MET311 4.6 130.1 1.0
ND2 G:ASN549 4.7 96.0 1.0
ND1 G:HIS262 4.7 83.7 1.0
CA G:GLY264 4.8 98.4 1.0
O1B G:ATP701 4.8 131.1 1.0
O3' G:ATP701 4.8 133.3 1.0
O G:GLY264 4.8 94.9 1.0
C G:GLY264 4.8 94.5 1.0
CB G:HIS262 4.9 81.6 1.0
C4 G:ATP701 4.9 131.8 1.0

Magnesium binding site 2 out of 8 in 9ofc

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Magnesium binding site 2 out of 8 in the Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three Intact Dimers


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three Intact Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg703

b:119.4
occ:1.00
 O G:HOH2003 1.8 99.2 1.0
O G:HOH2006 1.8 96.2 1.0
O3G G:ATP701 2.0 135.8 1.0
O3B G:ATP701 2.6 139.8 1.0
PG G:ATP701 2.9 146.1 1.0
O G:ASN317 3.3 105.3 1.0
O G:HOH2005 3.4 109.8 1.0
O G:GLY314 3.4 116.2 1.0
O2B G:ATP701 3.5 133.0 1.0
PB G:ATP701 3.6 141.5 1.0
O2G G:ATP701 3.8 133.1 1.0
O3A G:ATP701 3.9 133.4 1.0
CA G:GLY318 4.0 95.5 1.0
O G:GLY264 4.0 94.9 1.0
O1G G:ATP701 4.1 133.5 1.0
N G:SER319 4.2 102.5 1.0
C G:ASN317 4.3 100.9 1.0
MG G:MG702 4.4 129.2 1.0
C G:GLY314 4.6 115.0 1.0
C G:GLY318 4.6 92.7 1.0
N G:GLY318 4.7 97.0 1.0
H2' G:ATP701 4.9 132.1 1.0
O2A G:ATP701 4.9 133.1 1.0
OG G:SER319 4.9 119.3 1.0
O1B G:ATP701 4.9 131.1 1.0
PA G:ATP701 5.0 136.3 1.0
C G:GLY264 5.0 94.5 1.0

Magnesium binding site 3 out of 8 in 9ofc

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Magnesium binding site 3 out of 8 in the Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three Intact Dimers


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three Intact Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg701

b:141.9
occ:1.00
 O H:HOH804 1.8 115.0 1.0
O H:HOH805 1.9 127.5 1.0
O2B H:ATP703 1.9 152.9 1.0
O2A H:ATP703 3.2 150.8 1.0
PB H:ATP703 3.4 157.7 1.0
MG H:MG702 3.4 147.7 1.0
O H:HOH806 3.6 141.4 1.0
O3G H:ATP703 3.7 148.7 1.0
O3B H:ATP703 3.8 153.0 1.0
O H:GLY264 3.8 94.2 1.0
O H:GLY314 3.9 127.8 1.0
O3A H:ATP703 4.0 153.0 1.0
O2G H:ATP703 4.0 148.2 1.0
PG H:ATP703 4.2 154.9 1.0
PA H:ATP703 4.2 159.2 1.0
O H:ASN317 4.3 109.1 1.0
H2' H:ATP703 4.4 148.6 1.0
O1B H:ATP703 4.5 148.1 1.0
C H:GLY264 4.5 86.7 1.0
C H:GLY314 4.5 127.8 1.0
SD H:MET311 4.6 140.3 1.0
O5' H:ATP703 4.6 152.1 1.0
CA H:GLY314 4.7 125.6 1.0

Magnesium binding site 4 out of 8 in 9ofc

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Magnesium binding site 4 out of 8 in the Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three Intact Dimers


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three Intact Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg702

b:147.7
occ:1.00
 H2' H:ATP703 1.7 148.6 1.0
O5' H:ATP703 2.0 152.1 1.0
H8 H:ATP703 2.2 147.5 1.0
O2A H:ATP703 2.4 150.8 1.0
C2' H:ATP703 2.7 151.4 1.0
PA H:ATP703 2.7 159.2 1.0
C8 H:ATP703 3.0 149.3 1.0
C5' H:ATP703 3.2 147.9 1.0
H3' H:ATP703 3.4 148.8 1.0
MG H:MG701 3.4 141.9 1.0
C3' H:ATP703 3.4 151.2 1.0
H5'1 H:ATP703 3.4 147.1 1.0
O3A H:ATP703 3.5 153.0 1.0
C1' H:ATP703 3.6 151.7 1.0
N9 H:ATP703 3.6 152.7 1.0
O2' H:ATP703 3.6 152.4 1.0
O2B H:ATP703 3.7 152.9 1.0
C4' H:ATP703 3.8 149.3 1.0
O4' H:ATP703 3.9 149.7 1.0
O1A H:ATP703 3.9 148.1 1.0
H5'2 H:ATP703 4.0 147.9 1.0
N7 H:ATP703 4.0 146.2 1.0
SD H:MET311 4.0 140.3 1.0
PB H:ATP703 4.2 157.7 1.0
HO2' H:ATP703 4.3 149.0 1.0
CE H:MET311 4.4 129.3 1.0
O3B H:ATP703 4.5 153.0 1.0
H1' H:ATP703 4.5 148.6 1.0
O H:HOH806 4.7 141.4 1.0
H4' H:ATP703 4.7 147.8 1.0
O2G H:ATP703 4.7 148.2 1.0
O3' H:ATP703 4.7 150.0 1.0
O H:HOH803 4.8 120.5 1.0
ND2 H:ASN549 4.8 113.7 1.0
C4 H:ATP703 4.8 150.9 1.0
ND1 H:HIS262 4.8 99.6 1.0
CB H:HIS262 4.9 96.4 1.0
CG H:HIS262 4.9 97.5 1.0
O H:HOH805 4.9 127.5 1.0
HO3' H:ATP703 5.0 148.5 1.0
C5 H:ATP703 5.0 150.2 1.0

Magnesium binding site 5 out of 8 in 9ofc

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Magnesium binding site 5 out of 8 in the Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three Intact Dimers


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three Intact Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg702

b:170.7
occ:1.00
 H8 K:ATP701 1.9 189.6 1.0
O2A K:ATP701 1.9 188.0 1.0
O5' K:ATP701 2.1 191.9 1.0
PA K:ATP701 2.3 190.3 1.0
ND1 K:HIS262 2.4 116.9 1.0
C8 K:ATP701 2.8 190.7 1.0
H5'1 K:ATP701 2.8 189.0 1.0
C5' K:ATP701 3.0 189.6 1.0
CG K:HIS262 3.0 114.2 1.0
O1A K:ATP701 3.0 187.5 1.0
CB K:HIS262 3.2 115.7 1.0
CE1 K:HIS262 3.3 119.1 1.0
O K:HOH801 3.4 147.2 1.0
O4' K:ATP701 3.5 191.4 1.0
H2' K:ATP701 3.6 190.5 1.0
N7 K:ATP701 3.6 189.4 1.0
H5'2 K:ATP701 3.7 189.1 1.0
O3A K:ATP701 3.7 193.6 1.0
N9 K:ATP701 3.8 190.7 1.0
C4' K:ATP701 3.8 190.9 1.0
C1' K:ATP701 4.0 192.5 1.0
CD2 K:HIS262 4.0 118.1 1.0
C2' K:ATP701 4.1 192.2 1.0
NE2 K:HIS262 4.2 118.0 1.0
CA K:HIS262 4.3 114.1 1.0
C3' K:ATP701 4.5 192.0 1.0
H4' K:ATP701 4.6 189.1 1.0
OD1 K:ASN549 4.7 141.4 1.0
H3' K:ATP701 4.7 190.2 1.0
C5 K:ATP701 4.8 189.4 1.0
C4 K:ATP701 4.9 189.2 1.0
O K:ARG350 5.0 119.2 1.0
C K:HIS262 5.0 112.9 1.0
H1' K:ATP701 5.0 190.3 1.0

Magnesium binding site 6 out of 8 in 9ofc

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Magnesium binding site 6 out of 8 in the Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three Intact Dimers


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three Intact Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg703

b:156.9
occ:1.00
 O K:HOH806 1.9 178.1 1.0
O3G K:ATP701 2.1 191.2 1.0
O K:HOH804 2.2 157.4 1.0
O3B K:ATP701 2.9 193.6 1.0
PG K:ATP701 3.0 198.2 1.0
O2G K:ATP701 3.4 192.1 1.0
O K:GLY314 3.5 141.2 1.0
O K:ASN317 4.1 137.9 1.0
O K:GLY264 4.2 126.3 1.0
O K:HOH802 4.2 187.3 1.0
PB K:ATP701 4.3 193.9 1.0
O3A K:ATP701 4.3 193.6 1.0
O1G K:ATP701 4.3 193.3 1.0
C K:GLY314 4.4 141.7 1.0
O K:MET311 4.7 147.0 1.0
CA K:ASP315 4.9 158.7 1.0
O2B K:ATP701 4.9 188.8 1.0
N K:ASP315 5.0 158.9 1.0

Magnesium binding site 7 out of 8 in 9ofc

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Magnesium binding site 7 out of 8 in the Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three Intact Dimers


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three Intact Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg701

b:156.7
occ:1.00
 O L:HOH804 1.9 147.0 1.0
O L:HOH806 1.9 141.6 1.0
O L:ASN317 2.8 137.5 1.0
O L:GLY314 2.9 142.6 1.0
O2G L:ATP703 3.3 173.3 1.0
O3G L:ATP703 3.3 175.6 1.0
O L:HOH801 3.7 134.6 1.0
PG L:ATP703 3.8 178.1 1.0
CA L:GLY318 3.9 121.2 1.0
C L:ASN317 3.9 135.6 1.0
C L:GLY314 3.9 142.1 1.0
MG L:MG702 3.9 131.4 1.0
O3B L:ATP703 4.2 176.3 1.0
N L:GLY318 4.3 123.1 1.0
NH2 L:ARG312 4.4 138.4 1.0
O L:GLY264 4.5 119.5 1.0
CA L:ASP315 4.5 152.9 1.0
N L:ASP315 4.6 154.0 1.0
O2B L:ATP703 4.7 173.3 1.0
N L:SER319 4.8 137.0 1.0
O L:ASP315 4.8 151.3 1.0
C L:GLY318 4.8 122.5 1.0
CA L:GLY314 4.9 139.8 1.0
C L:ASP315 4.9 151.9 1.0
OD1 L:ASP315 5.0 156.3 1.0

Magnesium binding site 8 out of 8 in 9ofc

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Magnesium binding site 8 out of 8 in the Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three Intact Dimers


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryoem Structure of CAD1 Bound with CA4 and Atp, Hexamer with Three Intact Dimers within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg702

b:131.4
occ:1.00
 O L:GLY264 2.4 119.5 1.0
O2A L:ATP703 2.7 175.5 1.0
O L:HOH804 2.9 147.0 1.0
C L:GLY264 3.4 115.2 1.0
CA L:GLY265 3.9 107.0 1.0
MG L:MG701 3.9 156.7 1.0
N L:GLY265 4.0 105.7 1.0
CD1 L:ILE552 4.0 102.3 1.0
CE L:MET311 4.0 154.6 1.0
PA L:ATP703 4.2 176.4 1.0
OD1 L:ASN549 4.2 115.8 1.0
O2G L:ATP703 4.3 173.3 1.0
O3B L:ATP703 4.4 176.3 1.0
CA L:GLY264 4.4 113.6 1.0
O L:HOH801 4.4 134.6 1.0
H8 L:ATP703 4.7 172.7 1.0
H2' L:ATP703 4.7 174.0 1.0
O2B L:ATP703 4.8 173.3 1.0
O5' L:ATP703 4.9 174.1 1.0
O L:GLY314 4.9 142.6 1.0
CG1 L:ILE552 5.0 99.0 1.0
CG L:ASN549 5.0 114.2 1.0
O3A L:ATP703 5.0 176.6 1.0
O1A L:ATP703 5.0 172.0 1.0

Reference:

M.Roth, Y.Shu, D.Trasandidou, Y.Zhao, J.Van Der Oost, H.Li. Sequential Conformational Activation of A Carf-Fused Adenosine Deaminase By Cyclic Oligoadenylates To Be Published.
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