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Magnesium in PDB 9b0t: Cryo-Em Structure of E227Q Variant of UMTCK1 in Complex with Transition State Analog

Enzymatic activity of Cryo-Em Structure of E227Q Variant of UMTCK1 in Complex with Transition State Analog

All present enzymatic activity of Cryo-Em Structure of E227Q Variant of 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 E227Q Variant of UMTCK1 in Complex with Transition State Analog (pdb code 9b0t). 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 E227Q Variant of UMTCK1 in Complex with Transition State Analog, PDB code: 9b0t:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 9b0t

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Magnesium binding site 1 out of 8 in the Cryo-Em Structure of E227Q Variant of 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 E227Q Variant of UMTCK1 in Complex with Transition State Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:116.3
occ:1.00
 O1A A:ADP402 2.5 123.4 1.0
O2B A:ADP402 2.6 140.2 1.0
O1B A:ADP402 2.7 129.2 1.0
HH12 A:ARG231 2.7 110.4 1.0
PB A:ADP402 3.1 141.9 1.0
HH22 A:ARG231 3.5 116.9 1.0
O2 A:NO3403 3.5 151.2 1.0
NH1 A:ARG231 3.5 111.5 1.0
H5'1 A:ADP402 3.8 128.2 1.0
HZ3 A:TRP223 3.8 106.3 1.0
PA A:ADP402 3.8 134.4 1.0
O3A A:ADP402 4.0 140.7 1.0
HH11 A:ARG231 4.0 108.4 1.0
NH2 A:ARG231 4.1 120.9 1.0
OE2 A:GLU226 4.2 114.7 1.0
CZ A:ARG231 4.3 110.7 1.0
O3B A:ADP402 4.5 130.5 1.0
N A:NO3403 4.5 142.6 1.0
O5' A:ADP402 4.5 131.6 1.0
C5' A:ADP402 4.6 128.4 1.0
CZ3 A:TRP223 4.6 107.2 1.0
HH12 A:ARG315 4.7 135.8 1.0
HE21 A:GLN227 4.8 109.2 1.0
HG3 A:GLN227 4.8 104.6 1.0
OE1 A:GLU226 4.9 105.5 1.0
HH21 A:ARG231 4.9 117.4 1.0
O1 A:NO3403 5.0 128.7 1.0
CD A:GLU226 5.0 105.7 1.0
HB2 A:GLN227 5.0 104.4 1.0

Magnesium binding site 2 out of 8 in 9b0t

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Magnesium binding site 2 out of 8 in the Cryo-Em Structure of E227Q Variant of 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 E227Q Variant of UMTCK1 in Complex with Transition State Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:124.3
occ:1.00
 O1A B:ADP402 2.0 125.8 1.0
O2B B:ADP402 2.2 137.2 1.0
O1B B:ADP402 2.3 130.7 1.0
PB B:ADP402 2.6 141.9 1.0
PA B:ADP402 3.1 132.8 1.0
O3A B:ADP402 3.2 138.4 1.0
HH12 B:ARG231 3.3 109.7 1.0
H5'1 B:ADP402 3.3 127.7 1.0
HZ3 B:TRP223 3.6 105.2 1.0
O5' B:ADP402 3.7 130.2 1.0
O2 B:NO3403 3.8 153.3 1.0
HH22 B:ARG231 4.0 116.0 1.0
C5' B:ADP402 4.0 128.1 1.0
NH1 B:ARG231 4.0 111.2 1.0
O3B B:ADP402 4.1 129.8 1.0
HH12 B:ARG315 4.4 133.5 1.0
CZ3 B:TRP223 4.5 106.2 1.0
O2A B:ADP402 4.5 139.7 1.0
H5'2 B:ADP402 4.5 130.2 1.0
HH11 B:ARG231 4.5 107.8 1.0
OE2 B:GLU226 4.6 116.0 1.0
NH2 B:ARG231 4.6 120.0 1.0
HH2 B:TRP223 4.7 106.4 1.0
CZ B:ARG231 4.8 110.0 1.0
N B:NO3403 4.8 143.1 1.0
HH22 B:ARG125 4.8 111.8 1.0

Magnesium binding site 3 out of 8 in 9b0t

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Magnesium binding site 3 out of 8 in the Cryo-Em Structure of E227Q Variant of 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 E227Q Variant of UMTCK1 in Complex with Transition State Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:119.8
occ:1.00
 O1A C:ADP402 2.0 122.0 1.0
O1B C:ADP402 2.3 128.5 1.0
O2B C:ADP402 2.3 135.2 1.0
PB C:ADP402 2.7 139.4 1.0
PA C:ADP402 3.1 129.2 1.0
O3A C:ADP402 3.3 134.3 1.0
HH12 C:ARG231 3.3 110.5 1.0
H5'1 C:ADP402 3.3 124.2 1.0
HZ3 C:TRP223 3.6 105.4 1.0
O5' C:ADP402 3.7 126.4 1.0
O2 C:NO3403 3.8 151.5 1.0
HH22 C:ARG231 4.0 116.2 1.0
C5' C:ADP402 4.0 124.7 1.0
NH1 C:ARG231 4.0 111.9 1.0
O3B C:ADP402 4.1 127.6 1.0
HH12 C:ARG315 4.4 129.6 1.0
O2A C:ADP402 4.5 136.8 1.0
H5'2 C:ADP402 4.5 126.7 1.0
CZ3 C:TRP223 4.5 106.4 1.0
HH11 C:ARG231 4.5 108.3 1.0
OE2 C:GLU226 4.6 116.2 1.0
NH2 C:ARG231 4.6 120.7 1.0
HH2 C:TRP223 4.7 106.3 1.0
N C:NO3403 4.8 142.0 1.0
CZ C:ARG231 4.8 110.9 1.0
HH22 C:ARG125 4.8 110.3 1.0

Magnesium binding site 4 out of 8 in 9b0t

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Magnesium binding site 4 out of 8 in the Cryo-Em Structure of E227Q Variant of 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 E227Q Variant of UMTCK1 in Complex with Transition State Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg404

b:115.0
occ:1.00
 O2A D:ADP402 2.5 122.8 1.0
O2B D:ADP402 2.6 138.1 1.0
O3B D:ADP402 2.7 127.7 1.0
HH12 D:ARG231 2.7 109.4 1.0
PB D:ADP402 3.1 138.9 1.0
HH22 D:ARG231 3.5 115.8 1.0
O2 D:NO3403 3.5 152.2 1.0
NH1 D:ARG231 3.5 110.4 1.0
HZ3 D:TRP223 3.8 105.5 1.0
H5'1 D:ADP402 3.8 127.7 1.0
PA D:ADP402 3.8 134.1 1.0
O3A D:ADP402 4.0 139.7 1.0
HH11 D:ARG231 4.0 107.7 1.0
NH2 D:ARG231 4.1 119.6 1.0
OE2 D:GLU226 4.2 114.8 1.0
CZ D:ARG231 4.3 109.5 1.0
O1B D:ADP402 4.5 129.4 1.0
N D:NO3403 4.5 144.3 1.0
O5' D:ADP402 4.6 130.5 1.0
C5' D:ADP402 4.6 127.8 1.0
CZ3 D:TRP223 4.6 106.4 1.0
HH12 D:ARG315 4.7 135.1 1.0
HE21 D:GLN227 4.8 108.0 1.0
HG3 D:GLN227 4.8 103.8 1.0
HH21 D:ARG231 4.9 116.3 1.0
OE1 D:GLU226 4.9 105.2 1.0
O1 D:NO3403 5.0 130.2 1.0
CD D:GLU226 5.0 105.9 1.0
HB2 D:GLN227 5.0 104.0 1.0

Magnesium binding site 5 out of 8 in 9b0t

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Magnesium binding site 5 out of 8 in the Cryo-Em Structure of E227Q Variant of 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 E227Q Variant of UMTCK1 in Complex with Transition State Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg404

b:119.9
occ:1.00
 O2A E:ADP402 2.0 124.7 1.0
O2B E:ADP402 2.3 133.8 1.0
O3B E:ADP402 2.5 128.3 1.0
PB E:ADP402 2.7 139.9 1.0
PA E:ADP402 3.0 130.7 1.0
O3A E:ADP402 3.2 136.4 1.0
H5'1 E:ADP402 3.2 125.6 1.0
HH12 E:ARG231 3.4 109.3 1.0
O5' E:ADP402 3.5 128.4 1.0
HZ3 E:TRP223 3.7 104.9 1.0
O2 E:NO3403 3.8 151.2 1.0
C5' E:ADP402 3.9 126.4 1.0
HH22 E:ARG231 4.1 115.8 1.0
NH1 E:ARG231 4.2 110.7 1.0
O1B E:ADP402 4.2 129.1 1.0
H5'2 E:ADP402 4.3 128.2 1.0
HH12 E:ARG315 4.4 131.2 1.0
O1A E:ADP402 4.4 136.3 1.0
CZ3 E:TRP223 4.5 105.8 1.0
OE2 E:GLU226 4.6 116.1 1.0
HH11 E:ARG231 4.6 107.6 1.0
HH2 E:TRP223 4.7 105.6 1.0
NH2 E:ARG231 4.8 120.0 1.0
N E:NO3403 4.8 142.7 1.0
HH22 E:ARG125 4.9 111.0 1.0
CZ E:ARG231 4.9 109.8 1.0

Magnesium binding site 6 out of 8 in 9b0t

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Magnesium binding site 6 out of 8 in the Cryo-Em Structure of E227Q Variant of 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 E227Q Variant of UMTCK1 in Complex with Transition State Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg404

b:118.8
occ:1.00
 O2A F:ADP402 1.9 124.0 1.0
O3B F:ADP402 2.3 129.2 1.0
O2B F:ADP402 2.7 134.3 1.0
PB F:ADP402 2.8 138.9 1.0
PA F:ADP402 3.0 130.1 1.0
H5'1 F:ADP402 3.1 123.1 1.0
O3A F:ADP402 3.3 134.8 1.0
O5' F:ADP402 3.4 125.5 1.0
HH12 F:ARG231 3.5 109.9 1.0
HZ3 F:TRP223 3.7 104.6 1.0
C5' F:ADP402 3.7 123.8 1.0
O2 F:NO3403 3.9 151.4 1.0
HH22 F:ARG231 4.2 116.0 1.0
H5'2 F:ADP402 4.2 125.8 1.0
NH1 F:ARG231 4.2 111.1 1.0
O1B F:ADP402 4.3 126.0 1.0
O1A F:ADP402 4.4 134.9 1.0
HH12 F:ARG315 4.4 128.8 1.0
CZ3 F:TRP223 4.5 105.6 1.0
OE2 F:GLU226 4.6 115.6 1.0
HH2 F:TRP223 4.6 105.2 1.0
HH11 F:ARG231 4.7 107.8 1.0
NH2 F:ARG231 4.9 120.2 1.0
HH22 F:ARG125 4.9 110.2 1.0
N F:NO3403 4.9 142.3 1.0

Magnesium binding site 7 out of 8 in 9b0t

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Magnesium binding site 7 out of 8 in the Cryo-Em Structure of E227Q Variant of 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 E227Q Variant of UMTCK1 in Complex with Transition State Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg404

b:122.1
occ:1.00
 O2A G:ADP402 2.0 125.2 1.0
O2B G:ADP402 2.3 134.4 1.0
O3B G:ADP402 2.4 129.2 1.0
PB G:ADP402 2.7 140.4 1.0
PA G:ADP402 3.1 132.0 1.0
O3A G:ADP402 3.3 136.1 1.0
H5'1 G:ADP402 3.3 126.1 1.0
HH12 G:ARG231 3.3 111.4 1.0
O5' G:ADP402 3.6 127.9 1.0
HZ3 G:TRP223 3.7 106.6 1.0
O2 G:NO3403 3.8 151.5 1.0
C5' G:ADP402 4.0 126.2 1.0
HH22 G:ARG231 4.0 117.1 1.0
NH1 G:ARG231 4.1 112.6 1.0
O1B G:ADP402 4.2 129.3 1.0
HH12 G:ARG315 4.4 129.7 1.0
H5'2 G:ADP402 4.4 128.5 1.0
O1A G:ADP402 4.4 138.4 1.0
CZ3 G:TRP223 4.5 107.5 1.0
HH11 G:ARG231 4.5 109.2 1.0
OE2 G:GLU226 4.6 116.3 1.0
NH2 G:ARG231 4.7 121.2 1.0
HH2 G:TRP223 4.7 108.2 1.0
N G:NO3403 4.8 142.8 1.0
CZ G:ARG231 4.8 111.3 1.0
HH22 G:ARG125 4.8 112.5 1.0

Magnesium binding site 8 out of 8 in 9b0t

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Magnesium binding site 8 out of 8 in the Cryo-Em Structure of E227Q Variant of 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 E227Q Variant of UMTCK1 in Complex with Transition State Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg404

b:119.2
occ:1.00
 O1A H:ADP402 1.9 124.4 1.0
O1B H:ADP402 2.4 129.5 1.0
O2B H:ADP402 2.5 134.5 1.0
PB H:ADP402 2.8 140.5 1.0
PA H:ADP402 3.0 131.1 1.0
H5'1 H:ADP402 3.2 125.0 1.0
O3A H:ADP402 3.3 136.7 1.0
HH12 H:ARG231 3.5 111.6 1.0
O5' H:ADP402 3.5 127.3 1.0
HZ3 H:TRP223 3.7 105.8 1.0
C5' H:ADP402 3.8 125.6 1.0
O2 H:NO3403 3.9 153.7 1.0
HH22 H:ARG231 4.2 117.4 1.0
NH1 H:ARG231 4.2 112.5 1.0
O3B H:ADP402 4.3 129.2 1.0
H5'2 H:ADP402 4.3 128.1 1.0
O2A H:ADP402 4.4 137.3 1.0
HH12 H:ARG315 4.4 130.6 1.0
CZ3 H:TRP223 4.5 106.7 1.0
OE2 H:GLU226 4.6 116.3 1.0
HH11 H:ARG231 4.6 109.3 1.0
HH2 H:TRP223 4.6 107.0 1.0
NH2 H:ARG231 4.8 121.2 1.0
HH22 H:ARG125 4.9 112.6 1.0
N H:NO3403 4.9 143.6 1.0
CZ H:ARG231 5.0 111.0 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 11:13:01 2025

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