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Magnesium in PDB 9b14: Cryo-Em Structure of Human UMTCK1 in Complex with Transition State Analog

Enzymatic activity of Cryo-Em Structure of Human UMTCK1 in Complex with Transition State Analog

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Human UMTCK1 in Complex with Transition State Analog (pdb code 9b14). 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 Transition State Analog, PDB code: 9b14:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 9b14

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


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 Transition State Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:110.6
occ:1.00
 O3B A:ADP402 1.8 117.8 1.0
O2A A:ADP402 1.9 115.2 1.0
PA A:ADP402 3.2 109.4 1.0
PB A:ADP402 3.2 121.0 1.0
HH12 A:ARG231 3.3 97.7 1.0
O3A A:ADP402 3.5 110.5 1.0
H5'2 A:ADP402 3.8 107.8 1.0
HZ3 A:TRP223 3.9 94.8 1.0
OE2 A:GLU226 3.9 107.9 1.0
O2B A:ADP402 4.1 107.7 1.0
NH1 A:ARG231 4.1 96.8 1.0
O1A A:ADP402 4.2 116.7 1.0
O1B A:ADP402 4.2 122.9 1.0
H5'1 A:ADP402 4.3 110.8 1.0
O5' A:ADP402 4.3 108.5 1.0
HH12 A:ARG315 4.3 117.0 1.0
C5' A:ADP402 4.3 110.1 1.0
HH11 A:ARG231 4.4 94.3 1.0
HH22 A:ARG231 4.5 99.2 1.0
HG11 A:VAL320 4.6 121.1 1.0
OE1 A:GLU227 4.7 106.9 1.0
N6 A:CRN401 4.7 120.4 1.0
HG12 A:VAL320 4.7 123.1 1.0
CZ3 A:TRP223 4.8 96.2 1.0
CD A:GLU226 4.8 102.9 1.0
OE1 A:GLU226 4.9 100.0 1.0
HH11 A:ARG315 4.9 118.8 1.0
NH1 A:ARG315 5.0 119.3 1.0
HH2 A:TRP223 5.0 96.7 1.0

Magnesium binding site 2 out of 8 in 9b14

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


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 Transition State Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:108.7
occ:1.00
 O2A B:ADP402 2.1 113.9 1.0
O3B B:ADP402 2.1 115.5 1.0
PB B:ADP402 3.4 121.9 1.0
PA B:ADP402 3.5 110.7 1.0
O1B B:ADP402 3.8 129.9 1.0
OE2 B:GLU226 3.8 107.1 1.0
O3A B:ADP402 4.0 112.8 1.0
H5'2 B:ADP402 4.0 107.7 1.0
HZ3 B:TRP223 4.1 95.5 1.0
HH12 B:ARG315 4.3 119.0 1.0
O1A B:ADP402 4.3 120.1 1.0
OE1 B:GLU227 4.4 106.4 1.0
HG12 B:VAL320 4.4 124.7 1.0
HG11 B:VAL320 4.4 122.1 1.0
N6 B:CRN401 4.5 121.1 1.0
H5'1 B:ADP402 4.5 109.6 1.0
O5' B:ADP402 4.6 107.5 1.0
C5' B:ADP402 4.6 108.7 1.0
O2B B:ADP402 4.6 109.2 1.0
CD B:GLU226 4.7 103.1 1.0
HH21 B:ARG231 4.8 99.9 1.0
OE1 B:GLU226 4.8 99.9 1.0
HE B:ARG231 4.8 94.5 1.0
CG1 B:VAL320 4.9 124.0 1.0
CZ3 B:TRP223 5.0 96.4 1.0
NH1 B:ARG315 5.0 121.4 1.0

Magnesium binding site 3 out of 8 in 9b14

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


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 Transition State Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:110.2
occ:1.00
 O3B C:ADP402 1.9 119.5 1.0
O2A C:ADP402 1.9 112.3 1.0
PB C:ADP402 3.0 122.2 1.0
PA C:ADP402 3.2 107.9 1.0
O1B C:ADP402 3.3 128.0 1.0
HH12 C:ARG231 3.3 98.8 1.0
O3A C:ADP402 3.5 109.4 1.0
H5'2 C:ADP402 3.9 106.4 1.0
HZ3 C:TRP223 3.9 95.3 1.0
OE2 C:GLU226 4.0 106.4 1.0
O1A C:ADP402 4.1 117.5 1.0
NH1 C:ARG231 4.2 97.8 1.0
H5'1 C:ADP402 4.2 108.4 1.0
O2B C:ADP402 4.3 108.4 1.0
O5' C:ADP402 4.3 107.3 1.0
C5' C:ADP402 4.4 107.5 1.0
HG12 C:VAL320 4.4 122.6 1.0
HG11 C:VAL320 4.5 120.4 1.0
HH12 C:ARG315 4.5 116.8 1.0
HH11 C:ARG231 4.5 95.4 1.0
HH22 C:ARG231 4.5 100.1 1.0
N6 C:CRN401 4.7 120.6 1.0
OE1 C:GLU227 4.7 107.1 1.0
CZ3 C:TRP223 4.8 96.0 1.0
CG1 C:VAL320 4.9 122.0 1.0
CD C:GLU226 4.9 102.3 1.0
H C:VAL320 5.0 124.8 1.0
NH1 C:ARG315 5.0 118.5 1.0

Magnesium binding site 4 out of 8 in 9b14

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


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 Transition State Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg403

b:110.2
occ:1.00
 O2A D:ADP402 2.0 113.3 1.0
O3B D:ADP402 2.1 116.5 1.0
PB D:ADP402 3.4 121.6 1.0
PA D:ADP402 3.4 110.1 1.0
OE2 D:GLU226 3.8 108.3 1.0
O1B D:ADP402 3.9 127.2 1.0
O3A D:ADP402 4.0 112.3 1.0
H5'2 D:ADP402 4.0 108.2 1.0
HZ3 D:TRP223 4.0 95.4 1.0
O1A D:ADP402 4.3 119.4 1.0
HH12 D:ARG315 4.4 116.8 1.0
OE1 D:GLU227 4.4 105.8 1.0
HG11 D:VAL320 4.4 121.9 1.0
H5'1 D:ADP402 4.4 109.7 1.0
HG12 D:VAL320 4.4 124.2 1.0
N6 D:CRN401 4.5 120.1 1.0
C5' D:ADP402 4.5 109.6 1.0
O5' D:ADP402 4.5 108.1 1.0
O2B D:ADP402 4.6 108.5 1.0
CD D:GLU226 4.7 103.4 1.0
HH21 D:ARG231 4.8 100.2 1.0
HE D:ARG231 4.8 95.2 1.0
OE1 D:GLU226 4.8 100.1 1.0
CG1 D:VAL320 4.9 123.4 1.0
CZ3 D:TRP223 5.0 96.3 1.0

Magnesium binding site 5 out of 8 in 9b14

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


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 Transition State Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg403

b:108.5
occ:1.00
 O2A E:ADP402 2.0 113.8 1.0
O3B E:ADP402 2.1 116.6 1.0
PB E:ADP402 3.4 123.4 1.0
PA E:ADP402 3.4 110.1 1.0
OE2 E:GLU226 3.8 107.6 1.0
O1B E:ADP402 3.9 128.2 1.0
H5'2 E:ADP402 4.0 107.9 1.0
O3A E:ADP402 4.0 113.4 1.0
HZ3 E:TRP223 4.0 95.2 1.0
O1A E:ADP402 4.3 120.4 1.0
HH12 E:ARG315 4.3 118.0 1.0
OE1 E:GLU227 4.4 106.7 1.0
H5'1 E:ADP402 4.4 109.2 1.0
HG11 E:VAL320 4.4 122.2 1.0
HG12 E:VAL320 4.4 124.3 1.0
N6 E:CRN401 4.5 119.8 1.0
C5' E:ADP402 4.5 109.1 1.0
O5' E:ADP402 4.5 106.7 1.0
O2B E:ADP402 4.6 110.1 1.0
CD E:GLU226 4.7 103.0 1.0
HH21 E:ARG231 4.8 100.0 1.0
HE E:ARG231 4.8 94.9 1.0
OE1 E:GLU226 4.8 99.6 1.0
CG1 E:VAL320 4.9 123.8 1.0
CZ3 E:TRP223 5.0 96.1 1.0

Magnesium binding site 6 out of 8 in 9b14

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


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 Transition State Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg403

b:108.7
occ:1.00
 O2A F:ADP402 2.0 112.5 1.0
O3B F:ADP402 2.1 116.0 1.0
PB F:ADP402 3.4 122.8 1.0
PA F:ADP402 3.4 110.5 1.0
OE2 F:GLU226 3.8 107.3 1.0
O1B F:ADP402 3.9 128.5 1.0
O3A F:ADP402 4.0 113.1 1.0
H5'2 F:ADP402 4.0 107.7 1.0
HZ3 F:TRP223 4.0 95.2 1.0
O1A F:ADP402 4.3 121.1 1.0
HH12 F:ARG315 4.3 117.1 1.0
OE1 F:GLU227 4.4 106.3 1.0
HG11 F:VAL320 4.4 121.3 1.0
H5'1 F:ADP402 4.4 109.6 1.0
HG12 F:VAL320 4.4 123.8 1.0
N6 F:CRN401 4.5 120.9 1.0
C5' F:ADP402 4.5 108.7 1.0
O5' F:ADP402 4.5 106.8 1.0
O2B F:ADP402 4.6 109.6 1.0
HH21 F:ARG231 4.7 99.8 1.0
CD F:GLU226 4.7 103.1 1.0
HE F:ARG231 4.8 94.9 1.0
OE1 F:GLU226 4.8 99.5 1.0
CG1 F:VAL320 4.9 122.9 1.0
CZ3 F:TRP223 5.0 96.2 1.0

Magnesium binding site 7 out of 8 in 9b14

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


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 Transition State Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg403

b:111.0
occ:1.00
 O3B G:ADP402 1.9 117.0 1.0
O2A G:ADP402 2.1 113.0 1.0
PB G:ADP402 3.2 122.6 1.0
PA G:ADP402 3.4 109.2 1.0
O1B G:ADP402 3.6 129.7 1.0
O3A G:ADP402 3.8 112.3 1.0
OE2 G:GLU226 3.9 108.5 1.0
HZ3 G:TRP223 4.0 95.5 1.0
H5'2 G:ADP402 4.1 108.3 1.0
O1A G:ADP402 4.3 115.8 1.0
HG11 G:VAL320 4.3 121.4 1.0
HH12 G:ARG315 4.4 115.5 1.0
OE1 G:GLU227 4.4 106.5 1.0
O2B G:ADP402 4.4 109.9 1.0
N6 G:CRN401 4.5 119.3 1.0
O5' G:ADP402 4.6 109.5 1.0
HG12 G:VAL320 4.6 123.3 1.0
H5'1 G:ADP402 4.6 110.9 1.0
C5' G:ADP402 4.7 110.6 1.0
HH21 G:ARG231 4.7 99.8 1.0
HE G:ARG231 4.7 94.5 1.0
CD G:GLU226 4.8 103.5 1.0
OE1 G:GLU226 4.9 100.0 1.0
HH11 G:ARG315 4.9 116.8 1.0
CG1 G:VAL320 4.9 123.2 1.0
CZ3 G:TRP223 4.9 96.2 1.0
NH2 G:ARG231 5.0 100.5 1.0

Magnesium binding site 8 out of 8 in 9b14

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


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 Transition State Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg403

b:111.8
occ:1.00
 O3B H:ADP402 1.9 117.8 1.0
O2A H:ADP402 2.1 113.3 1.0
PB H:ADP402 3.2 121.1 1.0
PA H:ADP402 3.4 109.5 1.0
O1B H:ADP402 3.6 129.0 1.0
O3A H:ADP402 3.8 112.5 1.0
OE2 H:GLU226 3.9 107.2 1.0
HZ3 H:TRP223 4.0 96.5 1.0
H5'2 H:ADP402 4.1 108.6 1.0
O1A H:ADP402 4.3 116.4 1.0
HN32 H:CRN401 4.3 113.3 1.0
O2B H:ADP402 4.4 109.0 1.0
HG11 H:VAL320 4.4 120.2 1.0
OE1 H:GLU227 4.4 106.5 1.0
HN31 H:CRN401 4.5 115.5 1.0
O5' H:ADP402 4.6 109.0 1.0
HG12 H:VAL320 4.6 122.4 1.0
H5'1 H:ADP402 4.6 110.8 1.0
HH21 H:ARG231 4.7 99.7 1.0
N3 H:CRN401 4.7 117.8 1.0
C5' H:ADP402 4.7 110.5 1.0
HE H:ARG231 4.7 95.0 1.0
CD H:GLU226 4.8 103.3 1.0
OE1 H:GLU226 4.9 100.4 1.0
CZ3 H:TRP223 4.9 97.2 1.0
CG1 H:VAL320 5.0 121.9 1.0
NH2 H:ARG231 5.0 100.2 1.0
HH12 H:ARG315 5.0 115.3 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 11:12:50 2025

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