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Calcium in PDB 6twt: Crystal Structure of N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase

Protein crystallography data

The structure of Crystal Structure of N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase, PDB code: 6twt was solved by B.Imiolczyk, J.Czyrko-Horczak, K.Brzezinski, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.58 / 0.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.482, 73.980, 77.715, 90.00, 90.00, 90.00
R / Rfree (%) 10.5 / 12

Other elements in 6twt:

The structure of Crystal Structure of N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms
Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase (pdb code 6twt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase, PDB code: 6twt:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 6twt

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Calcium binding site 1 out of 5 in the Crystal Structure of N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:13.3
occ:0.90
 OD2 A:ASP223 2.4 9.9 0.5
O B:HOH551 2.4 23.2 1.0
O A:HOH456 2.4 21.1 1.0
O A:HOH558 2.5 23.8 1.0
OD2 A:ASP223 2.5 19.3 0.5
OE2 A:GLU152 2.5 14.2 1.0
OE2 B:GLU227 2.5 15.6 0.7
OE1 A:GLU152 2.6 13.3 1.0
OE1 B:GLU227 2.6 14.9 0.7
CD A:GLU152 2.9 12.2 1.0
OD1 A:ASP223 2.9 11.1 0.5
CD B:GLU227 2.9 13.4 0.7
OD1 A:ASP223 3.0 21.5 0.5
CG A:ASP223 3.0 9.9 0.5
CG A:ASP223 3.1 18.6 0.5
NE2 A:HIS122 4.3 13.8 1.0
O A:HOH411 4.4 38.5 1.0
O A:HOH566 4.4 35.8 1.0
CG A:GLU152 4.4 11.9 1.0
CG B:GLU227 4.5 12.6 0.7
NE2 B:HIS228 4.5 12.1 1.0
CB A:ASP223 4.5 9.9 0.5
O A:HOH474 4.5 16.2 1.0
O B:HOH535 4.5 36.7 1.0
O A:HOH512 4.6 12.8 1.0
CB A:ASP223 4.6 16.9 0.5
O B:HOH425 4.6 27.2 1.0
CE1 B:HIS228 4.8 12.0 1.0
CD2 A:HIS122 4.9 12.1 1.0

Calcium binding site 2 out of 5 in 6twt

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Calcium binding site 2 out of 5 in the Crystal Structure of N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:12.6
occ:0.80
 OD2 A:ASP95 2.4 15.4 1.0
O A:HOH600 2.4 20.1 1.0
OD2 A:ASP130 2.4 15.7 1.0
O A:HOH454 2.4 16.1 1.0
O A:HOH569 2.5 11.8 1.0
CG A:ASP95 3.4 11.4 1.0
CG A:ASP130 3.4 13.1 1.0
OD1 A:ASP95 3.8 12.2 1.0
CB A:ASP130 3.8 11.5 1.0
O A:HOH596 4.2 40.7 1.0
O A:GLY127 4.3 11.2 1.0
O A:HOH513 4.3 19.0 1.0
O A:HOH473 4.4 14.6 1.0
OD1 A:ASP130 4.5 15.4 1.0
O A:HOH479 4.6 11.1 1.0
CB A:ASP95 4.7 11.1 1.0
N A:ASP130 4.8 9.8 1.0
O A:HOH610 4.8 34.1 1.0
CG2 A:VAL155 4.8 12.5 1.0
CA A:ASP130 4.9 10.4 1.0

Calcium binding site 3 out of 5 in 6twt

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Calcium binding site 3 out of 5 in the Crystal Structure of N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:12.3
occ:0.90
 OD2 B:ASP223 2.4 13.9 1.0
O B:HOH597 2.4 19.4 1.0
O A:HOH535 2.4 22.9 1.0
O B:HOH580 2.5 20.6 1.0
OE2 A:GLU227 2.5 17.8 1.0
OE2 B:GLU152 2.5 12.4 1.0
OE1 B:GLU152 2.6 12.0 1.0
OE1 A:GLU227 2.6 16.7 1.0
OD1 B:ASP223 2.9 15.4 1.0
CD B:GLU152 2.9 11.1 1.0
CD A:GLU227 2.9 15.0 1.0
CG B:ASP223 3.0 12.4 1.0
O B:HOH403 4.2 30.4 1.0
NE2 B:HIS122 4.3 13.9 1.0
O B:HOH584 4.4 33.1 1.0
O A:HOH406 4.4 30.5 1.0
CG B:GLU152 4.4 10.3 1.0
CG A:GLU227 4.4 13.6 1.0
CB B:ASP223 4.5 12.0 1.0
NE2 A:HIS228 4.5 10.9 1.0
O B:HOH457 4.5 14.1 1.0
O B:HOH529 4.6 12.0 1.0
CE1 A:HIS228 4.8 11.2 1.0
CD2 B:HIS122 4.8 12.2 1.0

Calcium binding site 4 out of 5 in 6twt

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Calcium binding site 4 out of 5 in the Crystal Structure of N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:10.3
occ:0.80
 O B:GLY178 2.3 10.3 1.0
O B:HOH496 2.3 18.0 0.5
O B:HOH638 2.4 24.9 0.5
O B:HOH554 2.4 14.7 1.0
O B:HOH594 2.4 18.1 1.0
O B:HOH638 2.5 30.0 0.5
O B:HOH496 2.5 12.4 0.5
C B:GLY178 3.4 9.3 1.0
CA B:GLY178 4.2 10.8 1.0
OD2 B:ASP199 4.3 14.0 1.0
O B:HOH657 4.3 32.9 1.0
N B:GLY178 4.4 9.9 1.0
N B:PRO179 4.4 9.0 1.0
O B:HOH603 4.4 20.6 1.0
CA B:PRO179 4.5 9.0 1.0
O B:HOH578 4.5 18.3 1.0
O B:LEU180 4.5 9.6 1.0
C B:PRO179 4.8 8.1 1.0
O B:HOH459 4.8 22.4 0.5
C B:PHE177 4.9 8.3 1.0
O B:HOH660 4.9 18.8 1.0

Calcium binding site 5 out of 5 in 6twt

Go back to Calcium Binding Sites List in 6twt
Calcium binding site 5 out of 5 in the Crystal Structure of N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of N-Terminally Truncated Ndm-1 Metallo-Beta- Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca306

b:11.1
occ:0.65
 O B:HOH620 2.3 15.8 1.0
OD2 B:ASP95 2.4 13.7 1.0
OD2 B:ASP130 2.5 13.8 1.0
O B:HOH442 2.5 15.5 1.0
O B:HOH522 2.6 11.1 1.0
CG B:ASP95 3.3 11.3 1.0
O B:HOH401 3.4 15.4 0.5
O B:HOH553 3.4 26.4 0.5
CG B:ASP130 3.4 10.5 1.0
OD1 B:ASP95 3.6 13.0 1.0
CB B:ASP130 3.8 9.9 1.0
O B:HOH444 4.1 11.6 1.0
O B:HOH568 4.2 23.7 0.5
O B:HOH593 4.2 18.8 0.5
O B:GLY127 4.3 10.5 1.0
O B:HOH480 4.4 11.8 1.0
O B:HOH593 4.4 14.8 0.5
OD1 B:ASP130 4.5 15.7 1.0
O B:HOH486 4.7 10.2 1.0
CB B:ASP95 4.7 10.6 1.0
CG2 B:VAL155 4.7 10.1 1.0
N B:ASP130 4.8 8.9 1.0
O B:HOH401 4.8 23.3 0.5
O B:HOH680 4.8 29.5 1.0
O B:HOH667 4.8 31.7 0.8
CA B:ASP130 4.9 9.1 1.0

Reference:

J.E.Raczynska, B.Imiolczyk, M.Komorowska, J.Sliwiak, J.Czyrko-Horczak, K.Brzezinski, M.Jaskolski. Flexible Loops of New Delhi Metallo-Beta-Lactamase Modulate Its Activity Towards Different Substrates. Int.J.Biol.Macromol. 2020.
ISSN: ISSN 0141-8130
PubMed: 32353499
DOI: 10.1016/J.IJBIOMAC.2020.04.219
Page generated: Wed Jul 9 18:19:13 2025

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