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Magnesium in PDB 9b04: Cryo-Em Structure of Human UMTCK1 in Complex with Adp

Enzymatic activity of Cryo-Em Structure of Human UMTCK1 in Complex with Adp

All present enzymatic activity of Cryo-Em Structure of Human UMTCK1 in Complex with Adp:
2.7.3.2;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Human UMTCK1 in Complex with Adp (pdb code 9b04). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Cryo-Em Structure of Human UMTCK1 in Complex with Adp, PDB code: 9b04:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 9b04

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Magnesium binding site 1 out of 8 in the Cryo-Em Structure of Human UMTCK1 in Complex with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Human UMTCK1 in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:127.6
occ:1.00
 O3B A:ADP401 2.4 140.4 1.0
O2A A:ADP401 2.5 148.2 1.0
PB A:ADP401 3.6 148.0 1.0
PA A:ADP401 3.8 150.8 1.0
O1B A:ADP401 3.8 154.8 1.0
HH21 A:ARG231 3.9 100.0 1.0
HG3 A:GLU227 4.1 105.0 1.0
OE2 A:GLU226 4.1 109.5 1.0
O3A A:ADP401 4.2 138.4 1.0
H5'2 A:ADP401 4.6 140.1 1.0
HG11 A:VAL320 4.6 174.7 1.0
O1A A:ADP401 4.6 156.3 1.0
HZ3 A:TRP223 4.7 96.2 1.0
NH2 A:ARG231 4.7 102.0 1.0
HB2 A:GLU227 4.7 100.1 1.0
HE A:ARG231 4.7 92.8 1.0
O2B A:ADP401 4.8 131.3 1.0
HG12 A:VAL320 4.8 178.4 1.0
H5'1 A:ADP401 4.9 151.1 1.0
O5' A:ADP401 4.9 144.0 1.0
CG A:GLU227 5.0 108.5 1.0

Magnesium binding site 2 out of 8 in 9b04

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Magnesium binding site 2 out of 8 in the Cryo-Em Structure of Human UMTCK1 in Complex with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Human UMTCK1 in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:129.8
occ:1.00
 O3B B:ADP401 2.4 142.8 1.0
O2A B:ADP401 2.5 150.7 1.0
PB B:ADP401 3.6 149.2 1.0
PA B:ADP401 3.8 154.4 1.0
O1B B:ADP401 3.9 157.0 1.0
HH21 B:ARG231 3.9 99.5 1.0
HG3 B:GLU227 4.1 105.2 1.0
OE2 B:GLU226 4.2 109.3 1.0
O3A B:ADP401 4.2 142.2 1.0
H5'2 B:ADP401 4.6 140.9 1.0
HG11 B:VAL320 4.6 177.9 1.0
NH2 B:ARG231 4.7 101.7 1.0
HZ3 B:TRP223 4.7 95.0 1.0
HB2 B:GLU227 4.7 100.2 1.0
O1A B:ADP401 4.7 158.1 1.0
HE B:ARG231 4.7 93.1 1.0
O2B B:ADP401 4.8 130.5 1.0
HG12 B:VAL320 4.9 182.1 1.0
H5'1 B:ADP401 4.9 153.5 1.0
O5' B:ADP401 4.9 145.4 1.0
CG B:GLU227 5.0 108.4 1.0

Magnesium binding site 3 out of 8 in 9b04

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Magnesium binding site 3 out of 8 in the Cryo-Em Structure of Human UMTCK1 in Complex with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Human UMTCK1 in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:131.7
occ:1.00
 O3B C:ADP401 2.4 142.3 1.0
O2A C:ADP401 2.5 149.6 1.0
PB C:ADP401 3.6 147.7 1.0
PA C:ADP401 3.8 152.9 1.0
O1B C:ADP401 3.9 157.3 1.0
HH21 C:ARG231 3.9 99.9 1.0
HG3 C:GLU227 4.1 106.0 1.0
OE2 C:GLU226 4.1 109.3 1.0
O3A C:ADP401 4.2 140.2 1.0
H5'2 C:ADP401 4.6 141.2 1.0
HG11 C:VAL320 4.6 176.1 1.0
NH2 C:ARG231 4.7 101.1 1.0
O1A C:ADP401 4.7 156.6 1.0
HZ3 C:TRP223 4.7 95.8 1.0
HB2 C:GLU227 4.7 100.6 1.0
HE C:ARG231 4.7 93.7 1.0
O2B C:ADP401 4.8 129.0 1.0
HG12 C:VAL320 4.9 180.1 1.0
H5'1 C:ADP401 4.9 153.4 1.0
O5' C:ADP401 4.9 145.9 1.0
CG C:GLU227 5.0 109.3 1.0

Magnesium binding site 4 out of 8 in 9b04

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Magnesium binding site 4 out of 8 in the Cryo-Em Structure of Human UMTCK1 in Complex with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Human UMTCK1 in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:133.4
occ:1.00
 O2A D:ADP401 2.3 149.4 1.0
O3B D:ADP401 2.3 142.9 1.0
PB D:ADP401 3.5 149.5 1.0
PA D:ADP401 3.6 153.9 1.0
O1B D:ADP401 3.8 160.6 1.0
O3A D:ADP401 3.9 140.7 1.0
HH21 D:ARG231 4.1 99.7 1.0
OE2 D:GLU226 4.2 110.0 1.0
HG3 D:GLU227 4.3 105.0 1.0
H5'2 D:ADP401 4.4 140.1 1.0
O1A D:ADP401 4.5 157.7 1.0
HG11 D:VAL320 4.6 177.1 1.0
HZ3 D:TRP223 4.6 96.3 1.0
H5'1 D:ADP401 4.7 152.0 1.0
O5' D:ADP401 4.7 144.6 1.0
O2B D:ADP401 4.8 130.9 1.0
HG12 D:VAL320 4.8 180.8 1.0
HE D:ARG231 4.8 92.9 1.0
C5' D:ADP401 4.8 144.7 1.0
NH2 D:ARG231 4.9 101.8 1.0
HB2 D:GLU227 4.9 100.3 1.0
HH12 D:ARG315 4.9 152.9 1.0

Magnesium binding site 5 out of 8 in 9b04

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Magnesium binding site 5 out of 8 in the Cryo-Em Structure of Human UMTCK1 in Complex with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of Human UMTCK1 in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg402

b:133.8
occ:1.00
 O2A E:ADP401 2.3 150.1 1.0
O3B E:ADP401 2.3 144.8 1.0
PB E:ADP401 3.5 151.7 1.0
PA E:ADP401 3.6 155.2 1.0
O1B E:ADP401 3.9 159.9 1.0
O3A E:ADP401 4.0 142.3 1.0
HH21 E:ARG231 4.1 100.4 1.0
OE2 E:GLU226 4.2 110.5 1.0
HG3 E:GLU227 4.3 105.8 1.0
H5'2 E:ADP401 4.4 140.9 1.0
O1A E:ADP401 4.5 159.0 1.0
HZ3 E:TRP223 4.6 95.3 1.0
HG11 E:VAL320 4.6 176.4 1.0
H5'1 E:ADP401 4.7 152.7 1.0
O5' E:ADP401 4.7 145.9 1.0
O2B E:ADP401 4.8 132.0 1.0
HG12 E:VAL320 4.8 180.2 1.0
HE E:ARG231 4.8 93.1 1.0
C5' E:ADP401 4.8 146.1 1.0
NH2 E:ARG231 4.9 102.9 1.0
HB2 E:GLU227 4.9 100.5 1.0
HH12 E:ARG315 5.0 152.7 1.0

Magnesium binding site 6 out of 8 in 9b04

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Magnesium binding site 6 out of 8 in the Cryo-Em Structure of Human UMTCK1 in Complex with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of Human UMTCK1 in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg402

b:136.1
occ:1.00
 O2A F:ADP401 2.3 150.3 1.0
O3B F:ADP401 2.3 143.2 1.0
PB F:ADP401 3.5 150.6 1.0
PA F:ADP401 3.6 153.7 1.0
O1B F:ADP401 3.8 159.8 1.0
O3A F:ADP401 3.9 141.9 1.0
HH21 F:ARG231 4.0 100.1 1.0
OE2 F:GLU226 4.2 108.3 1.0
HG3 F:GLU227 4.3 106.8 1.0
H5'2 F:ADP401 4.4 141.5 1.0
O1A F:ADP401 4.5 157.7 1.0
HZ3 F:TRP223 4.6 95.9 1.0
HG11 F:VAL320 4.6 177.7 1.0
H5'1 F:ADP401 4.7 153.4 1.0
O5' F:ADP401 4.7 146.3 1.0
O2B F:ADP401 4.8 132.9 1.0
HE F:ARG231 4.8 93.2 1.0
HG12 F:VAL320 4.8 181.6 1.0
NH2 F:ARG231 4.9 102.3 1.0
C5' F:ADP401 4.9 146.8 1.0
HB2 F:GLU227 4.9 100.9 1.0
HH12 F:ARG315 5.0 152.4 1.0

Magnesium binding site 7 out of 8 in 9b04

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Magnesium binding site 7 out of 8 in the Cryo-Em Structure of Human UMTCK1 in Complex with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of Human UMTCK1 in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg402

b:135.8
occ:1.00
 O2A G:ADP401 2.3 148.8 1.0
O3B G:ADP401 2.3 143.4 1.0
PB G:ADP401 3.5 149.8 1.0
PA G:ADP401 3.6 150.7 1.0
O1B G:ADP401 3.8 159.0 1.0
O3A G:ADP401 4.0 139.1 1.0
HH21 G:ARG231 4.1 100.0 1.0
OE2 G:GLU226 4.2 111.0 1.0
HG3 G:GLU227 4.3 105.9 1.0
H5'2 G:ADP401 4.4 140.0 1.0
O1A G:ADP401 4.5 155.2 1.0
HG11 G:VAL320 4.6 176.7 1.0
HZ3 G:TRP223 4.6 96.6 1.0
H5'1 G:ADP401 4.7 151.7 1.0
O5' G:ADP401 4.7 144.3 1.0
O2B G:ADP401 4.8 133.0 1.0
HG12 G:VAL320 4.8 180.3 1.0
HE G:ARG231 4.8 93.5 1.0
C5' G:ADP401 4.9 145.0 1.0
NH2 G:ARG231 4.9 102.1 1.0
HB2 G:GLU227 4.9 100.5 1.0
HH12 G:ARG315 5.0 151.9 1.0

Magnesium binding site 8 out of 8 in 9b04

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Magnesium binding site 8 out of 8 in the Cryo-Em Structure of Human UMTCK1 in Complex with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of Human UMTCK1 in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg402

b:134.3
occ:1.00
 O2A H:ADP401 2.2 151.4 1.0
O3B H:ADP401 2.3 141.7 1.0
PB H:ADP401 3.5 149.5 1.0
PA H:ADP401 3.6 154.4 1.0
O1B H:ADP401 3.8 160.7 1.0
O3A H:ADP401 3.9 141.1 1.0
HH21 H:ARG231 4.0 99.4 1.0
OE2 H:GLU226 4.2 108.9 1.0
HG3 H:GLU227 4.3 106.0 1.0
H5'2 H:ADP401 4.4 141.8 1.0
O1A H:ADP401 4.5 157.9 1.0
HG11 H:VAL320 4.6 178.2 1.0
HZ3 H:TRP223 4.6 97.0 1.0
H5'1 H:ADP401 4.7 153.7 1.0
O5' H:ADP401 4.7 146.3 1.0
O2B H:ADP401 4.8 130.7 1.0
HG12 H:VAL320 4.8 181.9 1.0
HE H:ARG231 4.8 93.1 1.0
C5' H:ADP401 4.8 146.9 1.0
NH2 H:ARG231 4.8 101.2 1.0
HB2 H:GLU227 4.9 100.2 1.0
HH12 H:ARG315 4.9 152.1 1.0

Reference:

M.Demir, L.Koepping, Y.Li, L.Fujimoto, A.Bobkov, J.Zhao, T.Hitosugi, E.Sergienko. Structural Basis For Substrate Binding, Catalysis and Inhibition of Cancer Target Mitochondrial Creatine Kinase By A Covalent Inhibitor Structure 2025.
ISSN: ISSN 0969-2126
DOI: 10.1016/J.STR.2025.01.008
Page generated: Tue Feb 25 11:12:58 2025

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